From 6a1194245680aa63d5675fc3cab41959fa50f5da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Dar=C3=ADo=20Here=C3=B1=C3=BA?= Date: Wed, 13 May 2020 09:10:12 -0300 Subject: [PATCH] Minor fix on line 72 * minor formatting proposal on line 13 --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index eff51aa..e7d7338 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ Please open a new "issue" on github or contact authors Akdes.Harmanci@uth.tmc.ed # Installation -Type make to build BAFExtract. The executable is built under bin directory. The code is tested on various Unix based systems. +Type make to build BAFExtract. The executable is built under `bin` directory. The code is tested on various Unix based systems. # Usage @@ -69,4 +69,4 @@ fetchChromSizes hg19 > hg19.list ```{bash} mkdir test; samtools view SRR1295366.sorted.bam | ./bin/BAFExtract -generate_compressed_pileup_per_SAM stdin hg38.list test 50 0; ./bin/BAFExtract -get_SNVs_per_pileup hg38.list test ./hg38/ 20 4 0.1 test.snp ``` -Note: In the example above ./BAFExtract -generate_compressed_pileup_per_SAM uses mimunum mapping quality threshold 50. Depending on the aligner you used the MAPQ-Values can differ a lot and the setting of [Minimum mapping quality] to 50 could mean that no reads are surviving the filtering, only due to the aligners implementation of MAPQ. (acknowledgements to Tobias Tekath) +Note: In the example above ./BAFExtract -generate_compressed_pileup_per_SAM uses mininum mapping quality threshold 50. Depending on the aligner you used the MAPQ-Values can differ a lot and the setting of [Minimum mapping quality] to 50 could mean that no reads are surviving the filtering, only due to the aligners implementation of MAPQ. (acknowledgements to Tobias Tekath)