I am trying to load a vcf file (zipped and indexed in tabix) as a custom track in the UCSC Genome Browser and get the following message:
Error File 'PsvaMvd1_indels.vcf.gz' - Unrecognized format line 5 of somefile.gz: MT 1485 . N T 62.7 . DP=7;AF1=0.5;CI95=0.25,0.6875;DP4=0,0,2,3;MQ=28 PL:GT:GQ 25,3,25:0/1:22 0,0,0:0/1:3 0,0,0:0/1:3 0,0,0:0/1:3 25,3,25:0/1:22 25,3,25:0/1:22 0,0,0:0/1:3 45,6,45:0/1:39 (note: chrom names are case sensitive)
The gz and tbi files are on my computer. Can anyone please tell me what's wrong?
This is canine data. The reference I used to get vcf seems to contain MT as seen from below: $ grep ">" CanFam2.fasta
samtoolsVersion=0.1.16
fileformat=VCFv4.0
samtoolsVersion=0.1.16 (r963:234)
fileformat=VCFv4.0
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Thor.bam CobyKauf.bam Denver.bam WeeJock.bam F
Same error for other chr too, if I remove MT from vcf file.