File Info

Filename
.command.err
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/4c0d18e23be13f7dcb703b2a8d5b5e/.command.err
Size
741 bytes
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_HAPLOTYPER_RF_FILTER (659_bTo-N1-BDNA-1_B23KFG5LT4_1)
Attempt

Content

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INFO: Loading models...
INFO: Reading VCF: 659_bTo-N1-BDNA-1_B23KFG5LT4_1.entropy.vcf.gz
WARNING: Some variants missing INFO fields: {'QD'}
INFO: Loaded 31092 variants (28988 SNVs, 2104 INDELs)
INFO:   INDEL entropy: 1932 present, 172 missing (using -1 sentinel)
INFO: Annotating with BED files...
INFO:   Blacklist hits: 1094
INFO:   Low depth hits: 212
INFO:   Boosted exon hits: 5970
INFO:   SNV FP region hits: 3679
INFO:   INDEL FP region hits: 1377
INFO:   INDEL FP rate lookups (TSV): 15241 variant keys loaded
INFO:   RepeatMasker hits: 1637
INFO: Applying models...
INFO: Results: 26764 PASS (25394 SNV, 1370 INDEL), 4328 RF_FAIL
INFO: Writing output VCF: 659_bTo-N1-BDNA-1_B23KFG5LT4_1.haplotyper_rf.rf_filtered.vcf.gz
INFO: Done!