I used Samtools and bcftools to generate bcf files and then vcf files from the original BAM file containing RNA-seq data. Some of the publications i have read which make use of Samtools talk of filtering based on read quality, phred score, and depth. What are the typical parameters you use for these? The commands are as follows:
samtools view -bh -q(min_MapQ) in.bam > out.bam
samtools mpileup -uf in.ref.fa –Q(min_phred_Score) in.bam > out.bam
bcftools view var.raw.bcf | vcfutils.pl varFilter –D(max_depth) > var.flt.vcf
I did the alignment once using Tophat and once using BWA so that i have two sets of BAM files for the same RNA-seq data. Do the Samtools filtering parameters depend on the alignment algorithm used?
samtools view -bh -q(min_MapQ) in.bam > out.bam
samtools mpileup -uf in.ref.fa –Q(min_phred_Score) in.bam > out.bam
bcftools view var.raw.bcf | vcfutils.pl varFilter –D(max_depth) > var.flt.vcf
I did the alignment once using Tophat and once using BWA so that i have two sets of BAM files for the same RNA-seq data. Do the Samtools filtering parameters depend on the alignment algorithm used?
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