Call alternative base for each position in a bam file
1
2
Entering edit mode
4.2 years ago
sacha ★ 2.4k

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:

enter image description here

#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
bam calling • 1.6k views
ADD COMMENT
2
Entering edit mode

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

ADD REPLY
0
Entering edit mode
4.2 years ago

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1990 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6