From 951f690e1dc467ee54b0e1d4218bebf536468ff1 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 26 Nov 2016 08:47:48 +0100
Subject: [PATCH] samtools: add page (#1159)

---
 pages/common/samtools.md | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 pages/common/samtools.md

diff --git a/pages/common/samtools.md b/pages/common/samtools.md
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+# samtools
+
+> Tools for handling high-throughput sequencing (genomics) data.
+> Used for reading/writing/editing/indexing/viewing of data in SAM/BAM/CRAM format.
+
+- Convert a SAM input file to BAM stream and save to file:
+
+`samtools view -S -b {{input.sam}} > {{output.bam}}`
+
+- Take input from stdin (-) and print the SAM header and any reads overlapping a specific region to stdout:
+
+`{{other_command}} | samtools view -h - chromosome:start-end`
+
+- Sort file and save to BAM (the output format is automatically determined from the output file's extension):
+
+`samtools sort {{input}} -o {{output.bam}}`
+
+- Index a sorted BAM file (creates {{sorted_input.bam.bai}}):
+
+`samtools index {{sorted_input.bam}}`
+
+- Print alignment statistics about a file:
+
+`samtools flagstat {{sorted_input}}`
+
+- Count alignments to each index (chromosome / contig):
+
+`samtools idxstats {{sorted_indexed_input}}`
+
+- Merge multiple files:
+
+`samtools merge {{output}} {{input_1}} [{{input_2}}...]`
+
+- Split input file according to read groups:
+
+`samtools split {{merged_input}}`