If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 188.8.131.52
b) Exact command used:
c) Entire error log:
A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found.
reference contigs = [NC_000001.11, NT_187361.1, NT_187362.1, NT_187363.1, NT_187364.1, NT_187365.1, NT_187366.1, NT_187367.1, NT_187368.1, NT_187369.1, NC_000002.12, NT_187370.1,.........(where I omitted many more items)
features contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random,........
If not an error, choose a category for your question(REQUIRED):
a)How do I get the VCF files (PoN and germline source) matching my bam files and reference?
My bam files were generated by mapping fasta files to either NCBI grch38 or grch38patch13. Under both circumstances this error occured.
The previous handling process of data includes:
- Mapping fasta to references (index and dictionary generated with Samtools Faidx and GATK -launch createsequencedictionary. Not knowing why, but another set of index files generated with BWA index)
- Sam to Bam transfer and sort, with samtools
- Duplicate reads removal by MarkDuplicatesSpark
I have acquired the PoN and Germline source files from the following link. This is from a discussion threads.
The files I downloaded are
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