Hi, everyone!
I'm dealing with 14 sets of 81*2 data. After mapping them to reference genome by bwa 0.5.9-r16, I try to call variants using samtools 0.1.18. The strange thing is that all the thousands results of each sample are INDEL, though I can see there are SNPs by IGV.
Do you have any idea about this?
my command:
samtools mpileup -6AB -Q 30 -uf Egrandis_162.fa 1.rmdup.bam | bcftools view -bvcg - >1_30.RawVar.bcf 2>mpileup.log&
bcftools view 1_30.RawVar.bcf | vcfutils.pl varFilter -Q 30 -d 2 - > 1_30_30.FilterVar.vcf
I'm dealing with 14 sets of 81*2 data. After mapping them to reference genome by bwa 0.5.9-r16, I try to call variants using samtools 0.1.18. The strange thing is that all the thousands results of each sample are INDEL, though I can see there are SNPs by IGV.
Do you have any idea about this?
my command:
samtools mpileup -6AB -Q 30 -uf Egrandis_162.fa 1.rmdup.bam | bcftools view -bvcg - >1_30.RawVar.bcf 2>mpileup.log&
bcftools view 1_30.RawVar.bcf | vcfutils.pl varFilter -Q 30 -d 2 - > 1_30_30.FilterVar.vcf
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