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Old 03-12-2013, 10:50 AM   #1
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Location: West Lafayette

Join Date: Nov 2010
Posts: 5
Default Samtools - Missing SNPs in some chromosomes

Hello all,
I called SNPs using samtools(Version 0.1.18) on haploid genome and I found some interesting things. No SNPs were called for some chromosomes when SNP calling is carried out for entire genome however when the same parameters are used to call SNPs for those chromosomes individually, many SNPs are found.
Could you please let me know why would there be difference in number of SNPs when called for entire genome and individual chromosomes?

It would be really helpful if anyone of you could clarify how are SNPs called by samtools and explain why would there be difference (for SNPs called on entire genome and SNPs called on individual chromosomes). I have pasted samtools commands that I used:

1) Samtools command used to call SNPs from entire haploid genome
samtools mpileup -ABuf ref.fasta sample.bam | bcftools view -cvg -> sample.var.raw.vcf
No SNPs were called for chromosome1 using above command line.

2) Samtools command used to call SNPs for only chromosome1
samtools mpileup r chr1 -ABuf ref.fasta sample.bam | bcftools view -cvg -> sample_chr1.var.raw.vcf
Many SNPs were called for chromosome 1 using above command line.

Let me know your comments and suggestions.
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