From a bam file and a target bed file, I would like to extract each base count. I don't want to skip low frequency variant and sequencing errors. It seems I cannot do this using GATK or freebayes.
For instance, I would like to extract same data from IGV , even if I have a small allele frequency:
#CHROM POS DEPTH A C G T chr4 795890 40 2 0 38 0 .....
I tried with bcftools, but I didn't find this information:
chr4 795890 . G A,<*> 0 . DP=40;I16=18,15,1,0,1212,48324,66,4356,1980,118800,60,3600,574,12390,25,625;QS=0.952494,0.0475059,0;SGB=-0.379885;RPB=1;MQB=1;MQSB=1;BQB=1;MQ0F=0 PL 0,42,255,99,255,255