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hyunminkang / cleancall

Correction for DNA contamination in genotype calling
MIT License
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Strange symbols in "ALT" field #9

Open enabieva opened 5 years ago

enabieva commented 5 years ago

Hi (Thank you for answering my other question). cctools genotype writes strange symbols into the vcf file.
An example bam, index and output files can be found at https://cb.skoltech.ru/~enabieva/for_cleancall/ (the browser may complain about the certificate). An example of an offending line is on line 80 (chr20:310376). The reference is ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa The vcf file is the HapMap3.3 from the GATK Resource Bundle (ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/hapmap_3.3.hg38.vcf.gz)

Another issue I'm having is that if I don't restrict genotype to a particular chromosome, (chr20 in the example), it creates a Makefile target that's called just ".tbi" and then complains about it. I think it might have to do with prefixing the chromosome name with "chr".

enabieva commented 5 years ago

These symbols appear in areas where the input bams have no coverage.