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Loading Vcf-File-As-Custom-Track

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?

ucsc vcf
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updated by brentp brentp • written by Info_Nowise • Info_Nowise

1 answer

What organism is this for? Are you certain the chromosome "MT" exists in the UCSC tables?

You can see which chromosomes are available with mysql:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom from hg19.chromInfo"

where you'll replace hg19 with your organism. Not that for hg19 at least, the mitochondrial chromosome is "chrM", not "MT"

If this is not the problem then paste the header of the VCF into your question.

EDIT:

The chromosomes available in UCSC for canFam2 do not include "MT". You can check this with:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e "select chrom from canFam2.chromInfo"

so you'll have to convert the names in your VCF before displaying in UCSC.

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written by brentp brentp

This is canine data. The reference I used to get vcf seems to contain MT as seen from below: $ grep ">" CanFam2.fasta

MT dnarm:chromosome chromosome:BROADD2:MT:1:16727:1 38 dnarm:chromosome chromosome:BROADD2:38:1:26897727:1 35 dna_rm:chromosome chromosome:BROADD2:35:1:29542582:1 ......... Here is my VCF header :

fileformat=VCFv4.0

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.

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written by Info_Nowise • Info_Nowise

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