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andyrimmer / Platypus

Platypus Variant Caller
GNU General Public License v3.0
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callVariants problem with hg38 aligned bams #89

Open CPTPaso opened 4 years ago

CPTPaso commented 4 years ago

Hi,

I used platypus to call variants from hg19 aligned reads. This worked perfectly fine. I did the alignment with hg38, platypus ran through but only created a vcf containing the header and header description.

The log file says: "DEBUG - There are 0 filtered variant candidates in reads which overlap the region" for all regions. Therefore, it's not surpirising that the vcf output does not contain any varinats.

I already tried different samples, different hg38 references but nothing seems to work. The alignment pipeline is exactly the same as in the first run with hg19 except different reference. What I am doing wrong?

Best,

Patrick.

shuijingnvhaifl commented 1 year ago

Hi,

I used platypus to call variants from hg19 aligned reads. This worked perfectly fine. I did the alignment with hg38, platypus ran through but only created a vcf containing the header and header description.

The log file says: "DEBUG - There are 0 filtered variant candidates in reads which overlap the region" for all regions. Therefore, it's not surpirising that the vcf output does not contain any varinats.

I already tried different samples, different hg38 references but nothing seems to work. The alignment pipeline is exactly the same as in the first run with hg19 except different reference. What I am doing wrong?

Best,

Patrick.

Hi, Have you solved this problem? I have the same problem as you, my species is dog.