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Forum: Bioinformatics 02-06-2017, 11:15 PM
Replies: 636
Views: 126,103
Posted By Mat29
Thank you for developing BBMap. Could you please...

Thank you for developing BBMap. Could you please advise how to preprocess the output VCF to make it compatible with VCFAnnotator, SNPEff. I recieve "No gene feature" and "Chromososme is missing"...
Forum: Bioinformatics 01-28-2016, 02:13 AM
Replies: 36
Views: 25,296
Posted By Mat29
Please tell how to compare 300 VCF files using...

Please tell how to compare 300 VCF files using PySAM or smth else and to generate nonshared unique SNPs?
Forum: Bioinformatics 01-01-2016, 10:12 AM
Replies: 3
Views: 1,002
Posted By Mat29
Exclamation How to Run BBmap for many .fastaq files?

#!/bin/bash
./bbmap.sh ref=ref.fa # creating index file from the input reference
for i in {ls*.fastq}
do
./bbmap.sh in=i out={.}
done


I also tried using GNU parallel ls *.sra | xargs -I...
Forum: Bioinformatics 12-16-2015, 10:32 AM
Replies: 36
Views: 25,296
Posted By Mat29
Can Pysam call variants on .sam files?

Can Pysam call variants on .sam files?
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