I wondered if anyone could help me please? (apologies I can't give screen shots - as I work on a secure server).
I want to extract all the sample IDs that relate to a specific variant. I have a multisample VCF file for each chromosome.
I used to be able to extract this information using the code below and get all the IDs seperated by columns with the relevant VCF info (qual, filter, info, format, format_ouput). My variant text file (tab delimited) contains: Chr Pos Ref Alt
bcftools view -R "variants.txt" "mymultisample.vcf" > "newoutput.vcf"
However, all I get now is a few columns with lots of mixed mish mash of information that doesn't make sense. I also tried bcftools view -t, bcftools view -r, bcftools view -T, different formatting of the variant.txt file but no luck.
Thank you so so much for your help in advance.