Hi,
I had two Bam (1.bam, 2.bam) files from Bowtie2 and tried to call variants by Samtools. I have tried two procedures and they gave me different answers.
Procedure #1:
samtools mpileup -uf reference.fa bam1 bam2 | bcftools view -bvcg - > 12.bcf
bcftools view 12.bcf | vcfutils.pl varFilter -D100 12.flt.vcf
Procedure #2:
samtools merge 12_merged.bam 1.bam 2.bam
samtools mpileup -uf reference.fa 12_merged.bam | bcftools view -bvcg - > 12_merged.bcf
bcftools view 12_merged.bcf | vcfutils.pl varFilter -D100 12_merged.vcf
I can't figure out why. Please give some suggestions.
Thanks very much. Happy Thanks giving day.
I had two Bam (1.bam, 2.bam) files from Bowtie2 and tried to call variants by Samtools. I have tried two procedures and they gave me different answers.
Procedure #1:
samtools mpileup -uf reference.fa bam1 bam2 | bcftools view -bvcg - > 12.bcf
bcftools view 12.bcf | vcfutils.pl varFilter -D100 12.flt.vcf
Procedure #2:
samtools merge 12_merged.bam 1.bam 2.bam
samtools mpileup -uf reference.fa 12_merged.bam | bcftools view -bvcg - > 12_merged.bcf
bcftools view 12_merged.bcf | vcfutils.pl varFilter -D100 12_merged.vcf
I can't figure out why. Please give some suggestions.
Thanks very much. Happy Thanks giving day.
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