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comparison snpSift_filter.xml @ 4:fe23d90249ee

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Remove help error copied wiki: and is single ampersand
author Jim Johnson <jj@umn.edu>
date Wed, 20 Mar 2013 13:19:14 -0500
parents 2c595fea585c
children 192a236898f5
comparison
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3:3b0c657b852b 4:fe23d90249ee
49 49
50 * **(countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )** 50 * **(countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**
51 51
52 - *...or any heterozygous sample with coverage 25 or more*: 52 - *...or any heterozygous sample with coverage 25 or more*:
53 53
54 * **((countHet() > 0) &amp;&amp; (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )** 54 * **((countHet() > 0) &amp; (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) &amp; (QUAL >= 20)) | (QUAL >= 30 )**
55 55
56 - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*: 56 - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*:
57 57
58 * **isHom( GEN[0] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] )** 58 * **isHom( GEN[0] ) &amp; isVariant( GEN[0] ) &amp; isRef( GEN[1] )**
59 59