Call alternative base for each position in a bam file

Question

[sacha]

Hi,

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

[GenoMax]

Take a look at igvtools count included in IGV. Link to manual.

Answer 1

[dariober]

See also this thread Calculate The Frequency Of Nucleotides At Each Position In An Mpileup File I suggested there pysamstats and I'm still quite happy with it.

[sacha]

I tried pysamstats by the past . I was thinking it is only for read depths .