Closed nikhita-damaraju closed 4 months ago
My output folder does not contain a haplotagged BAM file. How can I generate this?
Here are the contents of the output folder:
HG002_ONT_R941_2_GRCh38_PEPPER_Margin_DeepVariant.chr20.vcf.gz HG002_ONT_R941_2_GRCh38_PEPPER_Margin_DeepVariant.chr20.vcf.gz.tbi HG002_ONT_R941_2_GRCh38_PEPPER_Margin_DeepVariant.chr20.visual_report.html intermediate_files/ DEEPVARIANT_OUTPUT_INDEL.vcf.gz PEPPER_VARIANT_OUTPUT_PEPPER.vcf.gz DEEPVARIANT_OUTPUT_INDEL.vcf.gz.tbi PEPPER_VARIANT_OUTPUT_PEPPER.vcf.gz.tbi DEEPVARIANT_OUTPUT_INDEL.visual_report.html PEPPER_VARIANT_OUTPUT_VARIANT_CALLING.vcf.gz DEEPVARIANT_OUTPUT_SNP.vcf.gz PEPPER_VARIANT_OUTPUT_VARIANT_CALLING.vcf.gz.tbi DEEPVARIANT_OUTPUT_SNP.vcf.gz.tbi PEPPER_VARIANT_OUTPUT_VARIANT_CALLING_INDEL.vcf.gz DEEPVARIANT_OUTPUT_SNP.visual_report.html PEPPER_VARIANT_OUTPUT_VARIANT_CALLING_INDEL.vcf.gz.tbi PEPPER_VARIANT_FULL.vcf.gz PEPPER_VARIANT_OUTPUT_VARIANT_CALLING_SNPs.vcf.gz PEPPER_VARIANT_FULL.vcf.gz.tbi PEPPER_VARIANT_OUTPUT_VARIANT_CALLING_SNPs.vcf.gz.tbi PEPPER_VARIANT_ONT_R941_GUPPY5_SUP_V8.pkl PHASED.PEPPER_MARGIN.chunks.csv PEPPER_VARIANT_ONT_R941_GUPPY5_SUP_V8.pkl.onnx logs/ 1_pepper.log 2_margin_haplotag.log 5.1_DeepVariant_SNP.log 5.2_DeepVariant_INDEL.log 6_merge_vcf.log
My output folder does not contain a haplotagged BAM file. How can I generate this?
Here are the contents of the output folder:
HG002_ONT_R941_2_GRCh38_PEPPER_Margin_DeepVariant.chr20.vcf.gz
HG002_ONT_R941_2_GRCh38_PEPPER_Margin_DeepVariant.chr20.vcf.gz.tbi
HG002_ONT_R941_2_GRCh38_PEPPER_Margin_DeepVariant.chr20.visual_report.html intermediate_files/ DEEPVARIANT_OUTPUT_INDEL.vcf.gz
PEPPER_VARIANT_OUTPUT_PEPPER.vcf.gz DEEPVARIANT_OUTPUT_INDEL.vcf.gz.tbi
PEPPER_VARIANT_OUTPUT_PEPPER.vcf.gz.tbi DEEPVARIANT_OUTPUT_INDEL.visual_report.html
PEPPER_VARIANT_OUTPUT_VARIANT_CALLING.vcf.gz DEEPVARIANT_OUTPUT_SNP.vcf.gz
PEPPER_VARIANT_OUTPUT_VARIANT_CALLING.vcf.gz.tbi DEEPVARIANT_OUTPUT_SNP.vcf.gz.tbi
PEPPER_VARIANT_OUTPUT_VARIANT_CALLING_INDEL.vcf.gz DEEPVARIANT_OUTPUT_SNP.visual_report.html
PEPPER_VARIANT_OUTPUT_VARIANT_CALLING_INDEL.vcf.gz.tbi PEPPER_VARIANT_FULL.vcf.gz
PEPPER_VARIANT_OUTPUT_VARIANT_CALLING_SNPs.vcf.gz PEPPER_VARIANT_FULL.vcf.gz.tbi
PEPPER_VARIANT_OUTPUT_VARIANT_CALLING_SNPs.vcf.gz.tbi PEPPER_VARIANT_ONT_R941_GUPPY5_SUP_V8.pkl
PHASED.PEPPER_MARGIN.chunks.csv PEPPER_VARIANT_ONT_R941_GUPPY5_SUP_V8.pkl.onnx logs/ 1_pepper.log
2_margin_haplotag.log
5.1_DeepVariant_SNP.log
5.2_DeepVariant_INDEL.log
6_merge_vcf.log