Export Consensus Seq.
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11.9 years ago
Shangool ▴ 10

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 • 4.2k views
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11.9 years ago

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?

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11.9 years ago
Shangool • 0

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

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There is a samtools.pl pileup2fq command in samtools

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