Changes between Version 9 and Version 10 of SOPs/vcf_manipulation

Timestamp:

01/20/16 14:13:55 (10 years ago)

Author:

byuan

Comment:

--

SOPs/vcf_manipulation

@@ -86 +86 @@
 vcf2bed < my_variants.vcf > my_variants.bed
 }}}
+
+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:
+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
+}}}
+
+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):
+java -jar /nfs/BaRC/apps/snpEff/Version_4/SnpSift.jar extractFields - CHROM POS REF ALT GEN[*].DP4  foo.vcf > DP4.vcf
+}}}