CRAM support in Mutect2 WDL #5668
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Codecov Report
@@ Coverage Diff @@
## master #5668 +/- ##
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- Coverage 87.049% 87.048% -0.001%
+ Complexity 31709 31708 -1
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Files 1940 1940
Lines 146172 146172
Branches 16130 16130
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- Hits 127242 127240 -2
- Misses 13042 13045 +3
+ Partials 5888 5887 -1
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takutosato
approved these changes
Feb 13, 2019
scripts/mutect2_wdl/mutect2_nio.wdl
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| String unfiltered_name = output_basename + "-unfiltered" | ||
| String filtered_name = output_basename + "-filtered" | ||
| String funcotated_name = output_basename + "-funcotated" | ||
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| String output_vcf_name = basename(tumor_bam, ".bam") + ".vcf" | ||
| String output_vcf_name = basename(tumor_reads, ".bam") + ".vcf" |
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This line should probably say String output_vcf_name = output_basename + ".vcf"
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@takutosato The engine team tells us not to run GATK tools on CRAM files for another several months while Joel fixes htsjdk bugs. This change lets the M2 WDL accept CRAMs by converting to BAM.
@LeeTL1220 This is needed for the SFARI induced pluripotency project.