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molecules · 01-10-2014, 11:07 AM

I'm using samtools mpileup and bcftools view to find variants. I'm perplexed why none of the alleles for any of the samples are shown as "missing...

amcrisan · 11-06-2013, 11:28 AM

Hi -

I am running a comparison between running samtools SNP calling in the multi sample mode, vs using it on each file individually. I seem...

CindyF · 09-12-2013, 08:56 AM

Hi all,

I read lots of papers about SNP calling and the different implementations (GATK, SAMtools, SOAPsnp, etc) in the last time. Something...

falarkys · 10-02-2012, 11:35 AM

I'm trying to get .vcf files from a .sam file via the following commands:

Code:

samtools view -bt ${fai} ${prefix}.sam > ${prefix}_unsorted.bam

...

Genomics101 · 07-10-2012, 06:36 AM

Greetings.

I am doing some SNP-/variant-calling, mapping to a somewhat divergent reference genome (probably about 1.5-2% different), but...

elfuser · 05-31-2012, 03:25 PM

Hello and sorry if this question has been asked before or it is super obvious.
I'm having a bit of a hard time finding out what the numbers mean...

elfuser · 05-31-2012, 08:40 AM

Hello:
I am using BWA + SAMtools/BCFtools to reference map assemble illumina reads and call SNPs in a bacterial genome respectively. I use the...

Marie_Noir · 04-16-2012, 05:22 AM

I generated one vcf file from 4 different bam-files (4 samples) and had a look at some variants in the vcf and in the IGViewer (IGV).

I...

Samtools and bcftools: Why aren't some of the calls "missing data".