From 0e2c1c843abac44f8ee9ae188e3378a2ce8c34fc Mon Sep 17 00:00:00 2001 From: Shifu Chen Date: Wed, 28 Dec 2016 11:24:41 +0800 Subject: [PATCH] Update README.md --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 2fa0fd3..79861dd 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,10 @@ EGFR-pos-7-55241707-18-c.2155G>A-p.G719S-COSM6252, GAAACTGAATTCAAAAAGATCAAAGTGCT EGFR-pos-7-55241707-18-c.2155G>T-p.G719C-COSM6253, GAAACTGAATTCAAAAAGATCAAAGTGCTG, T, GCTCCGGTGCGTTCGGCACGGTGTATAAGG ``` ## VCF-format mutation file -A standard VCF can be used as a mutation file, with file extension `.vcf` or `.VCF`. +A standard VCF can be used as a mutation file, with file extension `.vcf` or `.VCF`. If the mutation file is a VCF file, you should specify the `reference assembly file` by `-r `. For example the command can be: +```shell +mutscan -1 R1.fq -2 R2.fq -m target.vcf -r hg19.fa -h report.html +``` * if the VCF file is smaller than 100 records, all records can be scanned * if the VCF file has more than 100 records, you should add `--mark` in the command line, and then mark the wanted records with the `FILTER` column marked `M`. For example (note the M in the FILTER column): ```