Hi, How to get bases count (A, T, G, C) at a position in a vcf file?
Example: chr6 4064600 A 50 T 0 G 12 C 18
because some HLA types must be specific nucleotide at a specific position.
my command is:
bcftools mpileup -Ou -Q 0 -f $reference_genome $sampleName.sorted.bam | bcftools call -A -m -o Variants.txt
than I can get results like folloing:
chr1 4064600 . AGT A 25.5984 . INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AC=0;AN=2;DP4=0,0,0,1;MQ=60 GT:PL 0/0:4,3,
0
I found that DP4 value is "Number of 1) forward ref alleles; 2) reverse ref; 3) forward non-ref; 4) reverse non-ref alleles", but still can not get A:C:G:T, respectively.
Hi, How to get bases count (A, T, G, C) at a position in a vcf file?
Example: chr6 4064600 A 50 T 0 G 12 C 18
because some HLA types must be specific nucleotide at a specific position.
my command is:
bcftools mpileup -Ou -Q 0 -f $reference_genome $sampleName.sorted.bam | bcftools call -A -m -o Variants.txt
than I can get results like folloing:
chr1 4064600 . AGT A 25.5984 . INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AC=0;AN=2;DP4=0,0,0,1;MQ=60 GT:PL 0/0:4,3,
0
I found that DP4 value is "Number of 1) forward ref alleles; 2) reverse ref; 3) forward non-ref; 4) reverse non-ref alleles", but still can not get A:C:G:T, respectively.