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Old 01-16-2012, 03:01 AM   #1
Anjali
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Default Maximum read Depth in Samtools

Hi,
I wish to get the variants of my sequencing data using Samtools (vcfutils). For this I need to specify the maximum read depth in VarFilter function. I have no information of this from my Data. Can anybody tell me, how should I approach to its calculations, or considering default values??

Thanking you
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Old 01-16-2012, 03:09 AM   #2
ulz_peter
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You don't necessarily need to enter the exact number of your maximum coverage. That's just a way of speeding up analysis (AFAIK), for example if you enter 100 he would just use 100 alignments for SNP calling even if there is more available. I guess it depends on what you're looking for: for a normal diploid genome 100 should be sufficient...

Hope that helps,
Peter
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Old 01-16-2012, 03:15 AM   #3
Anjali
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Thanks a lot,,
I am working with Human Genome Assembly 18. According to Samtools a default value of 8000 should be used, but the purpose of it is to process all reads and to escape the time taking calculations,
when I take it as 8000 I get a different number of SNPs compared to taking 100 as the depth
what would you suggest on this?
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