Open WernaUVenema opened 1 year ago
I doubt that this is a bug. If you can compare the results from
samtools view -H [in.bam] | grep ^@SQ | head -n 30
and
tabix -H [in.vcf.gz] | grep contig | head -n 30
that would clarify the difference.
thats the vcf through grep
and therethe BAM
Did you reorder the VCF header too?
Yes, I did that manually using nano
I don't know what the problem is exactly here. I didn't run into this problem before. Is it possible that you can use demuxlet in popscle (which is recommended anyways) and see if the problem persists?
Dear all,
Although I already sorted the VCF file according to the chromosome order of the BAM file AND adjusted the header of the VCF file, I still get this error: " [E:int32_t cmdCramDemuxlet(int32_t, char**)] Your VCF/BCF files and SAM/BAM/CRAM files have different ordering of chromosomes. SAM/BAM/CRAM file has 1 before 10, but VCF/BCF file has 1 after 10 "
What could be the problem? Is there a bug?
Could anyone help me out here?
Thanks!