I am new to samtools and have been trying out several protocols on the web for variant calling. Can someone please tell me what the main difference is between this step of the deprecated protocol:
samtools view -u aln.sorted.bam | samtools pileup -vcf Ref.fa - > aln.sorted.raw.txt
and this step of the new recommended protocol?:
samtools mpileup -ugf Ref.fa aln.sorted.bam | bcftools view -bcvg - > aln.sorted.raw.bcf
I thought that both of these steps should return the unfiltered set of putative variants; however, the first one gives me substantially more variants than the second. I just want to make sure I am solid about what exactly is happening at these steps so that I can make informed decisions about what filtering is necessary downstream.
Thanks for your help!
samtools view -u aln.sorted.bam | samtools pileup -vcf Ref.fa - > aln.sorted.raw.txt
and this step of the new recommended protocol?:
samtools mpileup -ugf Ref.fa aln.sorted.bam | bcftools view -bcvg - > aln.sorted.raw.bcf
I thought that both of these steps should return the unfiltered set of putative variants; however, the first one gives me substantially more variants than the second. I just want to make sure I am solid about what exactly is happening at these steps so that I can make informed decisions about what filtering is necessary downstream.
Thanks for your help!
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