Dear Biostarts users,
This is my first time when I have to use variant-calling software/packages, so I would like to ask the opinion on mentioned below tools. How reliable are results produced by them?
My goal is to find appearance of A,C,T,G or DEL, INS at each base across chr1 (Not a whole genome). After researching on the topic "count frequency of A,C,T,G, Del, and Ins at each base" I ended up with the following options:
(1) samtools mpileup / bcftool call (2) bam-readcount (3) igvtools (4) pysamstats
The performance of the
IGVtools is same as the
Pysamstats, and I liked the output (it is clear and that's exactly what I need).
I understand that probably the
bam-readcount use another default options, therefore results are different to previous two. But I found the output results a bit messy for my task.
I also managed to get results in VCF format, but couldn't get desired frequency of A's, T's, C's, G's, DEL, INS. I saw the advice of using
pileup2baseindel, but it seems to be dated (Update 08/04/2012). Could anyone advice how to get frequency if A,C,T,G,Del, Ins from VCF format?
And what would you use if you task is to find only frequency of deletions, and NTs at each base?