Missing snv info files

[pinetree1]

The following command failed. Could you provide these files: snv_info/293T-snv_info.list1.bed and snv_info/293T-snv_info.list2.vcf ? Thanks!
python pmat-merge.py -i ${out_C_pmat} -f C -t T -r ${ref_genome_fa} -d 50 -D 100 --NoMutNumCutoff 2 --OmitTandemNumCutoff 2 -o ${out_CT_mpmat} --SNP snv_info/293T-snv_info.list1.bed,snv_info/293T-snv_info.list2.vcf 2> ${out_CT_log} &

[menghaowei]

font{ line-height: 1.6; } ul,ol{ padding-left: 20px; list-style-position: inside; } Sorry for late reply.The bed and vcf files are cell line SNV info, if you run Detect-seq pipeline with a different cell line, you need to run with the matched SNV info bed / vcf file.Moreover, the latest version of Detect-seq can run without those two file, and will not affect the final results. Bests.Haowei

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---- Replied Message ---- From Xuning ***@***.***> Date 02/16/2024 23:26 To ***@***.***> Cc ***@***.***> Subject [menghaowei/Detect-seq] Missing snv info files (Issue #2) The following command failed. Could you provide these files: snv_info/293T-snv_info.list1.bed and snv_info/293T-snv_info.list2.vcf ? Thanks! python pmat-merge.py -i ${out_C_pmat} -f C -t T -r ${ref_genome_fa} -d 50 -D 100 --NoMutNumCutoff 2 --OmitTandemNumCutoff 2 -o ${out_CT_mpmat} --SNP snv_info/293T-snv_info.list1.bed,snv_info/293T-snv_info.list2.vcf 2> ${out_CT_log} & —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>