Hi all,
I am using samtool mpileup to do SNP calling. I am experiencing some difficulties with the parameter settings.
For the single end data with a 200X coverage, samtools gave me the similar number of SNPs as SOAPsnp, GATK-UGT and Atlas-SNP2. However, for a pair-end data with 1000X coverage, samtools gave much less SNPs than the other callers.
For the pair end data, I tried the following code:
# samtools mpileup -ug -C50 -d1000 -f Feb11.2011.combined.25chr.fa 826T.fixed.cleaned.bam | bcftools view -bvcg - > 826T.samtool.mpileup.bcf
# bcftools view 826T.samtool.mpileup.bcf | vcfutils.pl varFilter -D1000 > 826T.samtool.mpileup.c50d1000.vcf
I tried the parameters "-C", "-d", and "-D" with several different numbers, but they all gave me the exactly same results. Based on the samtools instruction, the -d and -D are associated with coverage, and changing them around should make some difference. And I tried with older version (v.1.12) and new version (v.1.16) samtools. These parameter settings seem not working at all. Do anyone know what might go wrong? What should I do to get more SNPs called by samtools?
Any help appreciated!
I am using samtool mpileup to do SNP calling. I am experiencing some difficulties with the parameter settings.
For the single end data with a 200X coverage, samtools gave me the similar number of SNPs as SOAPsnp, GATK-UGT and Atlas-SNP2. However, for a pair-end data with 1000X coverage, samtools gave much less SNPs than the other callers.
For the pair end data, I tried the following code:
# samtools mpileup -ug -C50 -d1000 -f Feb11.2011.combined.25chr.fa 826T.fixed.cleaned.bam | bcftools view -bvcg - > 826T.samtool.mpileup.bcf
# bcftools view 826T.samtool.mpileup.bcf | vcfutils.pl varFilter -D1000 > 826T.samtool.mpileup.c50d1000.vcf
I tried the parameters "-C", "-d", and "-D" with several different numbers, but they all gave me the exactly same results. Based on the samtools instruction, the -d and -D are associated with coverage, and changing them around should make some difference. And I tried with older version (v.1.12) and new version (v.1.16) samtools. These parameter settings seem not working at all. Do anyone know what might go wrong? What should I do to get more SNPs called by samtools?
Any help appreciated!
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