Entering edit mode
8.3 years ago
dmitriev.nsu
•
0
Hi there,
I want to get information about allele frequency, but now I get info such as
CHROM POS N_ALLELES N_CHR {ALLELE:FREQ}
3 170968 2 2466 T:0.654907 G:0.345093
when I use vcftools --gzvcf input.vcf.gz --out out --keep individuals.txt --snps snps.txt --freq
How can I add info about snp (e.g. rs123456) to output file without reading file line by line?
I want to get something like that
CHROM POS ID N_ALLELES N_CHR {ALLELE:FREQ}
3 170968 rs123456 2 2466 T:0.654907 G:0.345093
Thank you
see https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotator.php#--dbsnp