I have been struggling with GATK 4 and feeling an acute lack of the command line pipelines available in previous versions. I took a look at the Tool Index and tried to make out the commands available from the https://github.com/gatk-workflows/gatk4-rnaseq-germline-snps-indels/blob/master/gatk4-rna-best-practices.wdl section
I have RNASeq data and I have used a GrCh38.p13 genomic reference not in the GATK resource bucket and currently I have processed around 600 samples with this same reference and followed till the Split n Cigar step with no problem
In the BaseRecalibrator step I get the following error :
a) GATK version
The Genome Analysis Toolkit (GATK) v22.214.171.124
HTSJDK Version: 2.21.2
Picard Version: 2.21.9
b) Exact GATK commands used
c) The entire error log if applicable.
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, NT_187371.1, NC_000003.12, NT_167215.1, NC_000004.12, NT_113793.3
I understand that the Reference is not matching to the dbSNP features
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, .....
The dbSNP files were downloaded from the Resource Bundle.Since re-mapping at this stage is not preferable I am feeling hopeless is there a way out of this?
Please help. Thank you very much
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