Changes between Version 11 and Version 12 of SOPs/vcf_manipulation

Timestamp:

07/19/16 09:55:19 (9 years ago)

Author:

gbell

Comment:

--

SOPs/vcf_manipulation

@@ -95 +95 @@
 Filter vcf with [http://snpeff.sourceforge.net/SnpSift.html#filter snpSift Filter ] function 
 {{{
-# only keep the variants with DV (number of high-quality non-reference bases) at least 1 in both the 1st and 2nd samples:
+# Only keep the variants with DV (number of high-quality non-reference bases) at least 1 in both the 1st and 2nd samples:
 java -jar /nfs/BaRC/apps/snpEff/Version_4/SnpSift.jar  filter " (GEN[0].DV>=1) & (GEN[1].DV>=1)" foo.vcf > s1.DVabove1.plus.s2.DVabove1.vcf
 }}}
@@ -101 +101 @@
 Extract fields from a VCF file to a TXT, tab separated format with [http://snpeff.sourceforge.net/SnpSift.html#Extract snpSift extractFields] function
 {{{
-# extract chromosome, position, reference base(s), alternate bases(s), all the samples' DP4 (number of high-quality ref-fwd, ref-reverse, alt-fwd, alt-reverse bases):
+# Extract chromosome, position, reference base(s), alternate bases(s), all the samples' DP4 (number of high-quality ref-fwd, ref-reverse, alt-fwd, alt-reverse bases):
 java -jar /nfs/BaRC/apps/snpEff/Version_4/SnpSift.jar extractFields - CHROM POS REF ALT GEN[*].DP4  foo.vcf > DP4.vcf
+
+# Similar command, but extract and split all PL fields
+java -jar /nfs/BaRC/apps/snpEff/Version_4/SnpSift.jar extractFields - CHROM POS REF ALT "GEN[*].PL[*]" foo.vcf > PL_values.vcf
 }}}