Hello,
I am new to this field and have couples of simple questions regarding SNP calling.
I used Bowie 2 to do the alignment for 10 libraries and call SNP with the following commands:
samtools mpileup -uDgf ref.fa sample1.sorted.bam sample2.sorted.bam ....sample10.sorted.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -d 30 > var.flt.vcf
Should I remove the unmapped reads and un-uniquely mapped reads from my Bam/Sam before employing Samtools mpileup to call variants?
If I need to use uniquely mapped read from Sam/ bam file, how can I extract them?
I would really appreciate your help
I am new to this field and have couples of simple questions regarding SNP calling.
I used Bowie 2 to do the alignment for 10 libraries and call SNP with the following commands:
samtools mpileup -uDgf ref.fa sample1.sorted.bam sample2.sorted.bam ....sample10.sorted.bam | bcftools view -bvcg - > var.raw.bcf
bcftools view var.raw.bcf | vcfutils.pl varFilter -d 30 > var.flt.vcf
Should I remove the unmapped reads and un-uniquely mapped reads from my Bam/Sam before employing Samtools mpileup to call variants?
If I need to use uniquely mapped read from Sam/ bam file, how can I extract them?
I would really appreciate your help