IGV export reads alignment sequence

[sadiexiaoyu]

Hi, All,

Does anybody know to use IGV to export track consensus sequences (including SNP)? But I just found how to copy one read sequence to clipboard... Could anyone help me?

Thanks!

Best,

Sadiexiaoyu

[dpryan]

I've never done this with IGV, but you should be able to create a pileup with samtools and then convert that to fastq (there's a perl script that at least used to come with samtools called "samtools.pl", it has a pileup2fq command). Fasta is just fastq sans the quality score, so you can just remove those lines.

[sadiexiaoyu]

I've never done this with IGV, but you should be able to create a pileup with samtools and then convert that to fastq (there's a perl script that at least used to come with samtools called "samtools.pl", it has a pileup2fq command). Fasta is just fastq sans the quality score, so you can just remove those lines.

Hi, dpryan,

Thank you for your reply! I dig the website, and it seems that IGV cannot extract consensus sequences yet... I will try samtools pipeline thanks!

Best,

Sadiexiaoyu