From d33a40cda558cd21e1b0f7e275a27551a6a0219f Mon Sep 17 00:00:00 2001 From: Giuseppe Narzisi Date: Fri, 18 Oct 2019 15:37:21 -0400 Subject: [PATCH] updated README --- README.md | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 810e118e..f6340549 100644 --- a/README.md +++ b/README.md @@ -64,13 +64,17 @@ The previous command shows an exemplary submission of multiple parallel lancet j ### Linked-Reads analysis -The recommended command line options for 10x Genomics linked-reads analysis are: +The recommended command line options for [10x Genomics](https://www.10xgenomics.com/) linked-reads analysis are: -~~~ -lancet **--linked-reads** **--primary-alignment-only** --tumor T.bam --normal N.bam --ref ref.fa --reg chr1 --num-threads 8 > out.vcf -~~~ +``` +lancet --linked-reads --primary-alignment-only --tumor T.bam --normal N.bam --ref ref.fa --reg chr1 --num-threads 8 > out.vcf +``` +where: + +* **linked-reads** activates the linked-reads mode to support LongRanger BAM format (e.g., BX and HP tags, etc.). +* **primary-alignment-only** forces the program to only use the primary alignment of each read for the analysis. -[LongRanger](https://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger) BAMs are directy supported, however, for improved accuarcy, we highly recommend to apply to the BAMs the [MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates) program from [Picard Tools](https://broadinstitute.github.io/picard/), which marks PCR duplicates more accurately than LongRanger. +[LongRanger](https://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger) BAMs are directy supported, however, for improved accuarcy, we highly recommend to process the BAMs with the [MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates) program from [Picard Tools](https://broadinstitute.github.io/picard/), which marks PCR duplicates more accurately than LongRanger. ### Output @@ -153,7 +157,7 @@ The final graph (after compression) containing one single variant is depicted be _____|\__,_|_| _|\___|\___|\__| Program: lancet (micro-assembly somatic variant caller) -Version: 1.1.1, October 18 2019 +Version: 1.1.0, October 18 2019 Contact: Giuseppe Narzisi Usage: lancet [options] --tumor --normal --ref --reg