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One stop MIP design and analysis
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SNPs not read for hg19 #10

Closed geertvandeweyer closed 4 months ago

geertvandeweyer commented 9 years ago

Hi,

mipgen does not read in snps for hg19-style dbsnp files (with the 'chr' notation). BED files of targets were correctly read, and results were provided, so it's just in the reading of the snp file, or fetching by tabix.

Best,

Geert

augustboyle commented 9 years ago

Hello,

Still having issues? Make sure that the variants are in proper vcf format and that the chromosome names in your file match the chromosome names in your reference. Those are definitely the most common issues.

Evan

On Mar 26, 2015, at 3:00 AM, geertvandeweyer notifications@github.com wrote:

Hi,

mipgen does not read in snps for hg19-style dbsnp files (with the 'chr' notation). BED files of targets were correctly read, and results were provided, so it's just in the reading of the snp file, or fetching by tabix.

Best,

Geert

— Reply to this email directly or view it on GitHub.

janrehker commented 9 years ago

Hi,

Not sure whether this is still causing trouble.. I just ran into a similar situation with mipgen. It seems that tabix was stumbling over the SNP file I got from dbSNP. It seems the issue was that the vcf was compressed in a way that is incompatible with tabix. For me the solution was to decompress the file with gunzip .vcf.gz, then recompressing it with bgzip .vcf To check if tabix was OK with that, I reindexed it with tabix -p vcf *.vcf.gz After that mipgen loaded the SNPs and created some alternative MIPs.

zpc975571872 commented 2 years ago

hi

Does the index created by tabix need to be placed in the MIPGEN folder? I don't understand why it keeps loading at 0snps

augustboyle commented 1 year ago

The index should be in the same directory as the VCF. Make sure the chromosome names match and tabix knows it is a VCF file.