Hi, everyone,
I am trying to call SNPs from a single .bam file by Samtools. From the .vcf output file, I found the allele frequency (AF1) is either 1 or 0.5. I can't figure out whether I did something wrong here. Has any one seen similar situation?
Call SNPs from a single alignment:
$> samtools mpileup –uf myreference.fasta myalignment.bam > tmp_output.bcf
$> bcftools view –bvcg tmp_output.bcf > raw.bcf
$> bcftools view > raw.vcf
$> vcfutils.pl varFilter –D100 raw.vcf > my_samtool_snps.vcf
thanks very much.
best,
shouhong
I am trying to call SNPs from a single .bam file by Samtools. From the .vcf output file, I found the allele frequency (AF1) is either 1 or 0.5. I can't figure out whether I did something wrong here. Has any one seen similar situation?
Call SNPs from a single alignment:
$> samtools mpileup –uf myreference.fasta myalignment.bam > tmp_output.bcf
$> bcftools view –bvcg tmp_output.bcf > raw.bcf
$> bcftools view > raw.vcf
$> vcfutils.pl varFilter –D100 raw.vcf > my_samtool_snps.vcf
thanks very much.
best,
shouhong
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