Hi! I have so popular question about problem with overlapping contigs. HaplotypeCaller writes:

reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM] reads contigs = []

But why?

So, I think I should tell about input.

The first, I download reference-genome from my sequencer. It is hg19. If I open this file, we can see:

chr1

So, It is ok because program see it.

Secondly, I have vcf-file from my sequencer. I drew attention to heder and coordinates. If I open this file, we can see:

contig='<'ID=chr1,length=249250621,assembly=hg19> contig='<'ID=chr2,length=243199373,assembly=hg19>
.....

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample 1

chr1 pos id and other info about SNP

Thirdly, the vcf-file was formed in sequencer with aforementioned reference-file.

I do not understand why HaplotypeCaller do not see contigs in vcf-file.