This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Export Consensus Seq.

I want to export my consensus sequence from IGV to look at the reads in BLAST. I could make consensus pileup file by SAMTools but the problem is that I can not convert pileup to fasta or fastq. Could you please tell me, is there anyway to export consensus seq.?

Many Regards

consensus igv samtools alignment
• 5,879 views • link
updated by Rm Rm • written by Shangool • Shangool

3 answers

The developer says (as of last year) IGV can't export, and a quick check of the manual seems to confirm this is still true. See this thread on Seqanswers:

http://seqanswers.com/forums/showthread.php?t=6469

Any reason why you can't use SAMtools (or your genotype caller of choice) to do this?

• 0 views • link
written by David Quigley David Quigley

HI Tanks for reply. I can not look at my consensus from SAMTOOLS, because it is in pileup format and I can not convert it to fastq and then pt the reads in BLAST. Do you think is there any way?

many tanks

• 0 views • link
written by Shangool • Shangool

There is a samtools.pl pileup2fq command in samtools

• 0 views • link
written by 2184687-1231-83- 2184687-1231-83-

How To Generate A Consensus Fasta Sequence From Sam Tools Pileup?

• 1 views • link
updated by Ram Ram • written by Rm Rm

Log in to answer this question.

More posts like this