Dear all,
i have a strange (for me) problem with generating variant calls by 'samtools mpileup' from a BAM file (attached in archive) generated with novoalign. Namely the base qualities are wrong (different as reported in BAM/SAM) when the reference is provided. Running the following command on the attached BAM:
'samtools mpileup -r chr14:68272021-68272021 test.bam'
yields:
chr14 68272021 N 23 acaCcCacacAAAACCCCACAC^gC ___QFF___]][_\___X\___W
but running:
'samtools mpileup -r chr14:68272021-68272021 -f hg19.fa test.bam'
yields:
chr14 68272021 C 23 a,a.,.a,a,AAAA....A.A.^g. !^!QFF!^!]!%!$^N^X$^!^A
The base quality values in the latter are different than those stored in BAM/SAM.
Any help will be appreciated.
Best Regards,
Jacek
i have a strange (for me) problem with generating variant calls by 'samtools mpileup' from a BAM file (attached in archive) generated with novoalign. Namely the base qualities are wrong (different as reported in BAM/SAM) when the reference is provided. Running the following command on the attached BAM:
'samtools mpileup -r chr14:68272021-68272021 test.bam'
yields:
chr14 68272021 N 23 acaCcCacacAAAACCCCACAC^gC ___QFF___]][_\___X\___W
but running:
'samtools mpileup -r chr14:68272021-68272021 -f hg19.fa test.bam'
yields:
chr14 68272021 C 23 a,a.,.a,a,AAAA....A.A.^g. !^!QFF!^!]!%!$^N^X$^!^A
The base quality values in the latter are different than those stored in BAM/SAM.
Any help will be appreciated.
Best Regards,
Jacek
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