From aff4bd0a808e7fc501aca9d8a151adf92f8a1ec3 Mon Sep 17 00:00:00 2001 From: Amie Radenbaugh Date: Mon, 1 Jun 2015 12:13:38 -0700 Subject: [PATCH] Update pysam version and added citation --- README.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index a5329af..fe1623c 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ you'll need python (version 2.7). RADIA uses samtools (version 0.1.18 or higher) to examine pileups of reads across each sample in parallel. You must install samtools prior to running RADIA. -3) pysam API (version 0.7.5)
+3) pysam API (version 0.8.1 and higher)
RADIA uses the pysam API during the filtering process. 4) BLAT
@@ -176,6 +176,13 @@ python mergeChroms.pyc patientId /radia/filtered/ /radia/filtered/ --gzip This will merge all of the files with the names: patientId_chr\*.vcf or patientId_chr\*.vcf.gz into one file called patientId.vcf or patientId.vcf.gz (if you specify the --gzip parameter). +=========== +CITATION +=========== +If you use RADIA, please site the method:
+Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D. (2014) RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection. PLoS ONE 9(11): e111516. doi:10.1371/journal.pone.0111516 + + ========= LICENSE =========