Hi Mali,
The 1000Genomes people tend to put many samples in a single BAM file separated through their Readgroup tags. GATK states VariantRecalibration needs a lot of SNPs to work smoothly, so since we analyse very few Exomes I had to switch to VariantFiltrator.
I'd do the analysis separately for each sample and look afterwards to combine the data.
In case you're searching for a disease causing gene in a set of patients I'd recommend to have a look at IBD2 (http://compbio.charite.de/contao/ind...cles/xibd.html). It could extract regions with same haplotypes for different patients. THat decreases the amount of SNPs drastically...
You're very welcome,
Peter
The 1000Genomes people tend to put many samples in a single BAM file separated through their Readgroup tags. GATK states VariantRecalibration needs a lot of SNPs to work smoothly, so since we analyse very few Exomes I had to switch to VariantFiltrator.
I'd do the analysis separately for each sample and look afterwards to combine the data.
In case you're searching for a disease causing gene in a set of patients I'd recommend to have a look at IBD2 (http://compbio.charite.de/contao/ind...cles/xibd.html). It could extract regions with same haplotypes for different patients. THat decreases the amount of SNPs drastically...
You're very welcome,
Peter
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