Error in opening VCF files

[joanne icc]

Hi - 

I have tried to open a VCF file obtained from 1000 genomes database. However, I get the following error message: 

Error loading /Users/-----/Downloads/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: /Users/-----/Downloads/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf

The following is the link I am trying to open on IGV - 

ALL.chrMT.phase3_callmom-v0_4.20130502.genotype..>

FYI I am using IGV on mac version 2.10.0 

Would greatly appreciate help with this - thanks in advance. 

Joanne 

[James Robinson]

It looks like you did not download the. complete VCF file, or there was some corruption during download.  However, even if you had the complete VCF file it is malformed, you would get a different message but it still would not be loadable.   The error message is

htsjdk.tribble.TribbleException$InternalCodecException: The following invalid GT allele index was encountered in the file: 0, for input source:....

There isn't much to be done about this.   You could raise an issue at https://github.com/samtools/htsjdk/issues, they might have some suggestions on fixing the file.   Include the link to the file, and the error message above.