Re: GT doubtDear Thomas
I used the command lines:
v.0.1.19samtools mpileup -q20 -Q20 -AB -ugf Ggallus.fa 1sort.bam 2sort.bam
3sort.bam 4sort.bam (...28 files) | bcftools view -bvcg - >
2014.raw.bcfbcftools view var2014.raw.bcf |vcfutils.pl varFilter -D99999 >
2014.vcf
v.1.2samtools mpileup -q20 -Q20 -AB -ugf Ggallus.fa 1sort.bam 2sort.bam
3sort.bam 4sort.bam (...28 files) | bcftools call -mv -Ov > sam_v1.2.vcf
thanksClarissa Boschiero
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