Alternative To "Samtools.Pl Pileup2Fq" For Consensus Generation?
1
4
Entering edit mode
10.7 years ago
Ketil 4.1k

I would like to generate a consensus based on mapping reads to a reference, but samtools doesn't fill in gaps or deal well with indels. Is there a good alternative available?

samtools consensus • 4.4k views
ADD COMMENT
1
Entering edit mode

So far as I know, you have to write your own.

ADD REPLY
0
Entering edit mode

Take a look here to see if this is what you are looking for.

ADD REPLY
1
Entering edit mode
10.6 years ago

as far as I know, to extract a consensus from mapping reads you must use a variant caller such as samtools' pileup, since what it does is not only to call the variants found, but to generate a "modified reference sequence" which is in fact the consensus of all your reads.

the fact that samtools' pileup doesn't deal with with indels could be solved with other variant caller, like GATK for instance, but unfortunately I don't know of any other that would fill the gaps where no reads are found. I think that lh3 is right, and that you have to write your own either from scratch (I wouldn't go that far) or by filling manually the gaps extracting the needed portions of the reference sequence for the missing gaps.

ADD COMMENT

Login before adding your answer.

Traffic: 1550 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