Mercurial > repos > iuc > pairtools_sort
view test-data/output_dups_pairs_markdups.pairsam @ 7:50d926b3f13d draft default tip
planemo upload for repository https://github.com/open2c/pairtools commit 89826caaf2e2bc933ef2ce407f21260ad69bc5c7
| author | iuc |
|---|---|
| date | Sun, 22 Dec 2024 15:41:44 +0000 |
| parents | 8ed44487c834 |
| children |
line wrap: on
line source
## pairs format v1.0.0 #sorted: chr1-chr2-pos1-pos2 #shape: upper triangle #genome_assembly: unknown #chromsize: chrI 230218 #chromsize: chrII 813184 #chromsize: chrIII 316620 #chromsize: chrIV 1531933 #chromsize: chrV 576874 #chromsize: chrVI 270161 #chromsize: chrVII 1090940 #chromsize: chrVIII 562643 #chromsize: chrIX 439888 #chromsize: chrX 745751 #chromsize: chrXI 666816 #chromsize: chrXII 1078177 #chromsize: chrXIII 924431 #chromsize: chrXIV 784333 #chromsize: chrXV 1091291 #chromsize: chrXVI 948066 #chromsize: chrM 85779 #samheader: @SQ SN:chrI LN:230218 #samheader: @SQ SN:chrII LN:813184 #samheader: @SQ SN:chrIII LN:316620 #samheader: @SQ SN:chrIV LN:1531933 #samheader: @SQ SN:chrIX LN:439888 #samheader: @SQ SN:chrM LN:85779 #samheader: @SQ SN:chrV LN:576874 #samheader: @SQ SN:chrVI LN:270161 #samheader: @SQ SN:chrVII LN:1090940 #samheader: @SQ SN:chrVIII LN:562643 #samheader: @SQ SN:chrX LN:745751 #samheader: @SQ SN:chrXI LN:666816 #samheader: @SQ SN:chrXII LN:1078177 #samheader: @SQ SN:chrXIII LN:924431 #samheader: @SQ SN:chrXIV LN:784333 #samheader: @SQ SN:chrXV LN:1091291 #samheader: @SQ SN:chrXVI LN:948066 #samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2 #samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2 #samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/6/8/8/dataset_688d7caa-53ad-49d2-ab0b-d5ff0c2f9a6e.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_3f551c40-c5f0-4546-9a95-9cff58b6eaf8.dat --output-dups /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_46064cb0-a915-4a2c-b434-30912a2c1c6e.dat --mark-dups --nproc-in 1 --nproc-out 1 PP:pairtools_sort-1.3 VN:1.1.0 #samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz #samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2 #samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2 #samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/6/8/8/dataset_688d7caa-53ad-49d2-ab0b-d5ff0c2f9a6e.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_3f551c40-c5f0-4546-9a95-9cff58b6eaf8.dat --output-dups /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_46064cb0-a915-4a2c-b434-30912a2c1c6e.dat --mark-dups --nproc-in 1 --nproc-out 1 PP:pairtools_sort-2.3 VN:1.1.0 #samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz #samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2 #samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2 #samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/6/8/8/dataset_688d7caa-53ad-49d2-ab0b-d5ff0c2f9a6e.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_3f551c40-c5f0-4546-9a95-9cff58b6eaf8.dat --output-dups /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_46064cb0-a915-4a2c-b434-30912a2c1c6e.dat --mark-dups --nproc-in 1 --nproc-out 1 PP:pairtools_sort-3.3 VN:1.1.0 #samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz #samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam #samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2 #samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2 #samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/6/8/8/dataset_688d7caa-53ad-49d2-ab0b-d5ff0c2f9a6e.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_3f551c40-c5f0-4546-9a95-9cff58b6eaf8.dat --output-dups /tmp/tmpp1v7bap4/job_working_directory/000/4/outputs/dataset_46064cb0-a915-4a2c-b434-30912a2c1c6e.dat --mark-dups --nproc-in 1 --nproc-out 1 PP:pairtools_sort-4.4 VN:1.1.0 #columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2 HWI-ST560:29:B0A7LABXX:2:1101:2692:4382 chrIII 80421 chrIII 80656 + - DD HWI-ST560:29:B0A7LABXX:2:1101:2692:4382161chrIII804216050M=80607236CTCTTCTAGCAGGAAGAGATCGTCCTTTTTACTGTCCTCGAATCCTACCGCCCFFFFFHHHHHGIIGIGIJIIJJJJJJJJIJJIJJIJJJIJIIFIJIINM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:2692:438281chrIII806076050M=80421-236ATCTTATATGCCTAATACAAAAAGAAGCTCACTAACATCAAAATCATTATHIGGFIIGIIJJJJJIHJJJJHHFIJJIHIFIJJJHGCC>332224D=:1NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU HWUSI-EAS1533_0033_FC:1:1:2403:20808 chrIV 497939 chrIV 498215 + - DD HWUSI-EAS1533_0033_FC:1:1:2403:2080897chrIV4979396036M=498180277CGCTTTCATTACTCGAATCCGTCAAAGACGCTTCTT4544588888C@@CC@CCC@@@C@@@C@CCC@C@CCNM:i:1MD:Z:0A35AS:i:35XS:i:0Yt:Z:UU HWUSI-EAS1533_0033_FC:1:1:2403:20808145chrIV4981806036M=497939-277GGCTGGTGAAGGAGTATTATTTACAATTCTAAAGCN@@C@@@@CC@CC@CC22C@@@CCCCC888886666)NM:i:1MD:Z:35T0AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:20583:3832 chrIV 623680 chrIV 623930 + - DD HWI-ST560:29:B0A7LABXX:2:1101:20583:3832161chrIV6236806050M=623881251TAAACAGTTAATGAAATCAGTTGTTACAAATGAGTTTCAATGCAGCTTAABBCFDFDDHHFCHGIII<ABHHHHIHFHFDGIIIIJJJJJGIIDHICGGGNM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:20583:383281chrIV6238814450M=623680-251GGATCATCTAGATGAAGAGTTGGACCTGACTGGGCCGATAAACAACTCACB909DHD?F?*?*GHFF???:*11IHHFAFFGFGC<23233322244141NM:i:3MD:Z:5G6G8T28AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:21049:12870 chrVII 395112 chrVII 395330 + - DD HWI-ST560:29:B0A7LABXX:2:1101:21049:1287097chrVII395112603S47M=395298219AAATTTTATCATAAAGATGAAAAACCTCGACCACGTTTTGCACATCAGCA##################################################NM:i:3MD:Z:9C9C4T22AS:i:32XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:21049:12870145chrVII3952986017S33M=395112-219TCGAAGGTAGACATCTTACTTGTAGTACCACAACTGAATGAAATCTTGCT####################EHDC4A3EA<3<,,9<?4C2:+3A8DD@<=NM:i:0MD:Z:33AS:i:33XS:i:0Yt:Z:UU HWUSI-EAS1533_0033_FC:1:1:2739:11140 chrVIII 403630 chrVIII 403904 + - DD HWUSI-EAS1533_0033_FC:1:1:2739:11140161chrVIII4036305836M=403869275NGCTTGCTACTTTGTGCGAGCTTGATATGCAGGACA(22/277777C@CCCCC@@CCC@@C@@@CC@@@@@CNM:i:2MD:Z:0A15T19AS:i:30XS:i:0Yt:Z:UU HWUSI-EAS1533_0033_FC:1:1:2739:1114081chrVIII4038696036M=403630-275AGTTTTTCTGACGATCTGAAGTCTGTTTACCAAGCA@444CCCC@@CC@@@CC@CCCCCCCC877773333=NM:i:1MD:Z:35T0AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:20782:17358 chrXIII 538121 chrXIII 544653 - - DD HWI-ST560:29:B0A7LABXX:2:1101:20782:17358177chrXIII5380726050M=5446046533GAGCTTCATCGGATGTTGGTGAGTGATGAATATCACGGTAAAGAATACAA3HEGED86)6GGHCHGDC2A<AEHA<<AHGHHDC1HHDHD?FAFDB=@@BNM:i:1MD:Z:0A49AS:i:49XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:20782:17358113chrXIII5446046050M=538072-6533TATTGCGCTGACTTCGTTATCATTCAAGCTAACTAGTTCTTCCTCGTCTGAFGAGEGHF?0=HGFDB<CC4:1)FIIHGFF<C<2222230000044111NM:i:1MD:Z:23G26AS:i:45XS:i:0Yt:Z:UU HWUSI-EAS1533_0033_FC:1:1:1306:18143 chrXIII 794677 chrXIII 794956 + - DD HWUSI-EAS1533_0033_FC:1:1:1306:18143161chrXIII7946776036M=794921280NAGGTGGCAGCATAGCACTGTAATGAGATATATTAA%&(&)*)*+,:1:::<<<:0::3::@@@5@@@:@@@NM:i:1MD:Z:0G35AS:i:35XS:i:0Yt:Z:UU HWUSI-EAS1533_0033_FC:1:1:1306:1814381chrXIII7949216036M=794677-280GGCTAGGCCAGTTAATACAAACGCTGAAACGGAATG####################################NM:i:1MD:Z:35C0AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:19177:20440 chrXV 1012747 chrXV 1012994 + - DD HWI-ST560:29:B0A7LABXX:2:1101:19177:2044097chrXV10127476050M=1012945248GATCTGCTTATTAAATCTGGCATAATAAAGTTGATTGTCTTGACGTTGCA11+44224222222<C<AEI:CBEIGIBH><FCHIBFHGHIGIII8?FFHNM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:19177:20440145chrXV10129456050M=1012747-248AACTTTTAACTCGGGAAATATGTATCACTATACTAAAAAACATTAATTTABFIGGGIIGGG@CBCFBCHHIHHH@FF<DF<FFE?DAHFCFA+?DBD@@?NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:15890:13657 chrXVI 416774 chrXVI 486947 - - DD HWI-ST560:29:B0A7LABXX:2:1101:15890:13657113chrXVI4167255150M=48689870174AGGGAGTAACAACGGATCGCAGTCAAATGAACTTCAGATACGGTATAAGC#######?9?93???@/@?<>)<@>=>89933).@?=22202))222000NM:i:3MD:Z:2T18T20T7AS:i:37XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:15890:13657177chrXVI4868984850M=416725-70174GAGAAACTTTTCATCAAAGCTAAAAGGCACTCACACAAGCCTTCCCGTCCB8BD>BF?*D>D?<GCG?*)@@IGBC*?1C1C2FAAGDDF<))DDA+=B=NM:i:3MD:Z:19A6T19T3AS:i:36XS:i:0Yt:Z:UU