I am trying to use Genmod for our pipeline, but while loading VCF generated by Freebayes and annotated by VEP, I am getting error,
“SyntaxError: One of the contig lines is malformed: ##contig=”
I understand this is due to missing contig length from the contig, if I manually modify header to “##contig=” or if I remove all contig info from header. It works fine.
Since, Freebayes doesn’t mentions contig length in multi-sample variant calling. Is there any way to get rid of this error in Genmod. Without need of additional formatting?
Also, how the information from contig line is used in Genmod??
moonso
commented
7 years ago
I am trying to use Genmod for our pipeline, but while loading VCF generated by Freebayes and annotated by VEP, I am getting error, “SyntaxError: One of the contig lines is malformed: ##contig=”
I understand this is due to missing contig length from the contig, if I manually modify header to “##contig=” or if I remove all contig info from header. It works fine.
Since, Freebayes doesn’t mentions contig length in multi-sample variant calling. Is there any way to get rid of this error in Genmod. Without need of additional formatting? Also, how the information from contig line is used in Genmod??