conversion to .vcf files
1
0
Entering edit mode
8.0 years ago
Chenglin ▴ 230

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       .
next-gen SNP • 1.9k views
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Entering edit mode

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.

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Entering edit mode
8.0 years ago
Laura ★ 1.8k

Does the -recode option work for this?

http://vcftools.sourceforge.net/documentation.html#newvcf

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