gtc2vcf
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freeseek
Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
Hi Giulio, The array Finngen2 Axiom custom array from ThermoFisher was used for genotyping in our project. We would like to convert the .CEL files to a .vcf file to...
I have a dataset that I am trying to convert to gtc but ran in to an error using bcftools and idat2gtc version 1.20. GEO accession is GSM5579064 and an...
Hi @freeseek Following up on #68, I was wondering if it may be feasible for you to include an Illumina_genotype tag in the FORMAT field? I see that based on...
Hi @freeseek , What does 0 and 1 represent for ALLELE_A and ALLELE_B in the VCF INFO? It seems like the Picard tools GtcToVcf implementation write alleles themselves in the...
A separate issue from the results in #64 is that 0.5-0.8% of markers could not be mapped from hg19 to hg38. While I think some percentage will be skipped anyway....
Hello @freeseek Is this a known issue that coordinates for CNV loci may be incorrectly/differently presented via SourceSeq mapping workflow? Since I have large set of chips and samples to...
Hi @freeseek I note that there are some indel records that gtc2vcf initially writes them but then `bcftools norm --check-ref x` filters them out. However, I was comparing to the...
I see that typically gtc2vcf does a fantastic job in infering the coordinates with the SourceSeq mapping workflow. However, I note that in some cases when SourceSeq maps to different...
The pseudo-autosomal regions is often annotated in the Illumina's CSV manifest as `XY` chrom. gtc2vcf probably recode them as chrom `X` in the output vcf: https://github.com/freeseek/gtc2vcf/blob/224e7c60b81188342a029ec89f3777537fa7b4f6/gtc2vcf.h#L138-L143 However, it may be...
Hi @freeseek Would it be feasible for you to release a new conda version based on the current dev version 1.20? My department uses a SnakeMake wrapper to do some...