Test-drive the GATK tools and Best Practices pipelines on Terra
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Help with BaitDepthWalker analysis
I am trying to get the coverage data using BaitDepthWalker tool:
java -jar recapseg-18.104.22.168/coverage.jar -T BaitDepthWalker --input_file normal_aln_IndelRealigned_ReorderedSam.bam --intervals zebrafish_zv9_core.baits_merged.bed --out normal_aln_IndelRealigned_Covdata --bed zebrafish_zv9_core.baits_merged.bed --reference_sequence danRer7.fa
The error message I get is:
ERROR MESSAGE: Input files zebrafish_zv9_core.baits_merged.bed and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
I used picard tool - ReorderSam on the input BAM, but still get the same error.
Could you please help.