Question: vcftools subset data missing all the information in FORMAT column
1
gravatar for MAPK
3.5 years ago by
MAPK1.4k
United States
MAPK1.4k wrote:

I know most of you would suggest me to use either bedtool or bcftools, but I tried a lot with these but could not get full information in my subset vcf file where I intend to extract the SNPs with all column information and updated AC, DP values etc. in my_bed.bed file. When I tried this with bedtool, I couldn't process the file due to conflicting AC= column values (it does not change in the subset data), So I am trying to get this done using vcftools. However, vcftools is also not immune to this problem as I am still missing most of the FORMAT column information (AC=0;AF=0.00054;AN=312;BaseQRankSum=-2.079;DP=40153;Dels=0.00;FS=1.621;HRun=0;HaplotypeScore=0.2550)

The command I am using to extract using vcftool is :

for file in *.vcf.gz; do
vcftools --gzvcf $file --recode --recode-INFO-all --bed /dir_for_bed_file/my_bed.bed --out  "${file}".vcf
done

Can someone please clarify the fuss here or if I am missing anything in my command line?

vcftools • 1.3k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by MAPK1.4k
1
gravatar for MAPK
3.5 years ago by
MAPK1.4k
United States
MAPK1.4k wrote:

Ok figured it out: It was missing --recode --recode-INFO-all.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by MAPK1.4k
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