I am interested in calling SNPs for some alignment data that I have. I am looking at solutions with
samtools mpileup and
I noticed that freebayes has an option to specify how many observations have to support a variant before it is called (the
Is there something similar for the
samtools mpileup option?
I've been using
samtools as follows:
samtools mpileup -uf reference.fasta Sample_sorted.bam -d 8000 | bcftools call -mv -Oz -o variants.vcf
However, I don't know how many observations supported the resulting variants.
An example SNP call from the above command is as follows:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample_sorted.bam Ecoli_genome 5159 . A G 228 . DP=303;VDB=0.658475;SGB=-0.693147;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0;AC=2;AN=2;DP4=0,1,120,171;MQ=60 GT:PL 1/1:255,255,0 Ecoli_genome 5162 . A T 228 . DP=310;VDB=0.633206;SGB=-0.693147;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,120,172;MQ=60 GT:PL 1/1:255,255,0 ...
Any insight is appreciated!