SAM/BAM/CRAM file has 1 before 10, but VCF/BCF file has 1 after 10

[WernaUVenema]

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!

[hyunminkang]

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.

[WernaUVenema]

thats the vcf through grep

[WernaUVenema]

and therethe BAM

[hyunminkang]

Did you reorder the VCF header too?

[WernaUVenema]

Yes, I did that manually using nano

[hyunminkang]

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?

[iaradsouza1]

You can use picard to sort your VCF based on your bam file and update the dictionary: statgen/popscle#42