I know it is a stupid question, but I'm a beginner of snp calling and really confused.
I run samtools and bcftools get vcf files like this
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT accepted_hits.bam
1 565286 . C T 222 . DP=27;VDB=2.078631e-01;AF1=1;AC1=2;DP4=0,0,14,12;MQ=40;FQ=-105 GT:PL:GQ 1/1:255,78,0:99
However, I not only want AF1 (Max-likelihood estimate of the first ALT allele frequency), but also want AF (allele frequency). How can I get a result containing both information?
I run samtools and bcftools like this:
samtools mpileup -ugf /data/Genomes/Homo_sapiens/Homo_sapiens_assembly19.fasta accepted_hits.bam | bcftools view -bvcg - > SRR1294493.bcf
bcftools view SRR1294493.bcf | vcfutils.pl varFilter -D 44 > SRR1295163.vcf
Thanks a lot.