Mercurial > repos > blankenberg > naive_variant_caller
annotate test-data/fake_phiX174_reads_1_test_out_2.vcf @ 17:6be51647d31a draft default tip
"planemo upload for repository https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/master/tools/naive_variant_caller commit 3e2fca43a0b119b34befa5d7642a07682d1d77af"
author | blankenberg |
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date | Thu, 05 Dec 2019 12:23:12 -0500 |
parents | 07e71cf6c8ef |
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rev | line source |
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07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
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1 ##fileformat=VCFv4.3 |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
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changeset
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2 ##source=Naive Variant Caller version 0.0.4 |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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3 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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4 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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5 ##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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7 ##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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8 ##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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9 ##FORMAT=<ID=SB,Number=1,Type=Float,Description="Strand Bias"> |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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10 ##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts"> |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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11 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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12 phiX174 1411 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=1, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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13 phiX174 1412 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=3, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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14 phiX174 1413 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=5, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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15 phiX174 1414 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=6, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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16 phiX174 1415 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=7, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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17 phiX174 1416 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=8, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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18 phiX174 1417 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=9, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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19 phiX174 1418 . T . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+T=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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20 phiX174 1419 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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21 phiX174 1420 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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22 phiX174 1421 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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23 phiX174 1422 . T . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+T=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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24 phiX174 1423 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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25 phiX174 1424 . C A . . AC=7;AF=0.7;SB=+Inf GT:AC:AF:SB:NC 1/0:7:0.7:+Inf:+A=7,+C=3, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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26 phiX174 1425 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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27 phiX174 1426 . T . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+T=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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28 phiX174 1427 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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29 phiX174 1428 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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30 phiX174 1429 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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31 phiX174 1430 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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32 phiX174 1431 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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33 phiX174 1432 . T . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+T=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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34 phiX174 1433 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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35 phiX174 1434 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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36 phiX174 1435 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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37 phiX174 1436 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
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38 phiX174 1437 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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39 phiX174 1438 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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40 phiX174 1439 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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41 phiX174 1440 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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42 phiX174 1441 . T . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+T=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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43 phiX174 1442 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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44 phiX174 1443 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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45 phiX174 1444 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
diff
changeset
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46 phiX174 1445 . C . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+C=10, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
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47 phiX174 1446 . C T . . AC=3;AF=0.3;SB=+Inf GT:AC:AF:SB:NC 0/1:3:0.3:+Inf:+C=7,+T=3, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
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48 phiX174 1447 . T A . . AC=2;AF=0.222222222222;SB=+Inf GT:AC:AF:SB:NC 0/0:2:0.222222222222:+Inf:+A=2,+T=7, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
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49 phiX174 1448 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=7, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
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50 phiX174 1449 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=5, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
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51 phiX174 1450 . T . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+T=4, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
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52 phiX174 1451 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=3, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
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53 phiX174 1452 . A . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+A=2, |
07e71cf6c8ef
planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/naive_variant_caller commit 56487ac8b5d91755e44d4e326105cdb9e409a66c
blankenberg
parents:
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54 phiX174 1453 . G . . . AC=.;AF=.;SB=0.0 GT:AC:AF:SB:NC 0/0:.:.:0.0:+G=1, |