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Search: Posts Made By: Andrew Beckerman
Forum: Bioinformatics 07-19-2012, 12:24 AM
Replies: 1
Views: 3,332
Posted By Andrew Beckerman
Perhaps a solution myself # generate mpilup,...

Perhaps a solution myself

# generate mpilup, say with two bams

samtools mpileup -B a.bam b.bam > out.mpileup

# Then use awk to filter on the depth of coverage columns (i.e. $4 and $7 for two...
Forum: Bioinformatics 07-18-2012, 05:39 AM
Replies: 1
Views: 3,332
Posted By Andrew Beckerman
Filter mpileup for high depth of coverage without bcftools/vcfutils

Hi

I am working with Illumina paired end read data, several populations. I am creating an mpileup from several .bam files, each from a different population. I would like to exclude candidate...
Forum: Bioinformatics 07-18-2012, 05:14 AM
Replies: 1
Views: 3,175
Posted By Andrew Beckerman
I sorted this.... it was a problem with -q...

I sorted this.... it was a problem with -q arguments in different functions not matching.
Forum: Bioinformatics 07-06-2012, 01:15 AM
Replies: 1
Views: 3,175
Posted By Andrew Beckerman
samtools view and mapq

I am working with paired end Illumina resequencing data from multiple populations.

My workflow involves samtools view -q to generate bamfiles with specific mapq score thresholds, samtools...
Forum: Introductions 07-06-2012, 12:59 AM
Replies: 0
Views: 806
Posted By Andrew Beckerman
Hello

Coming to visit from Sheffield, UK. Working with pooled, multi population resequencing data.
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