conversion to .vcf files
Dear all,
I used the following vcftools command to generate a file, which I wanted to use as a input file for SnpEff. However, I found that the file generated from using vcftools is not .vcf file (see below). Does anyone know how to convert the file to .vcf file? Thank you very much!
The command I used to generate the file:
vcftools --gzvcf sorted.vcf1.gz --gzdiff sorted.vcf2.gz --diff-site --out _1_vs_2
The format of the file:
CHROM POS1 POS2 IN_FILE REF1 REF2 ALT1 ALT2
1 996 . 1 N . A .
1 997 . 1 N . A .
1 998 . 1 N . A .
1 999 . 1 N . C .
1 1000 . 1 N . C .
1 1058 . 1 TAA . TAAA .
1 . 1077 2 . T . C
1 . 1078 2 . AAACCCTAA . AAACCCTAACCCTAA
1 . 1078 2 . A . T
1 . 2843 2 . GAAAA . GAAAAA
1 5292 . 1 A . AC,ACAG .
1 5323 . 1 TC . TGATAGATGTGCTCC .
1 11535 . 1 A . C .
1 11541 . 1 T . C .
1 . 21546 2 . T . A
1 . 22105 2 . CGG . CG
1 23314 . 1 GTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC . GTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC .
1 23320 . 1 ATCT . ATCTGTCT .
1 23337 . 1 TCTA . TCTAACTA .
1 . 26689 2 . GTTTTTTTTTTT . GTTTTTTTTTT
1 31071 31071 B A A G G
1 31478 . 1 C . T .
1 answer
Does the -recode option work for this?
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It'd be simpler if you stated exactly what your goal was in using vcftools --gzdiff. My guess is that you wanted to filter out shared variants, in which case that's not the command you want.