bwa: add page

pages/linux/bwa.md

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+# bwa
+
+> Burrows-Wheeler Alignment tool.
+> Short, low-divergent DNA sequences mapper against a large reference genome, such as the human genome.
+> More information: <https://github.com/lh3/bwa>.
+
+- Index the reference genome:
+
+`bwa index {{path/to/reference.fa}}`
+
+- Map single-end reads (sequences) to indexed genome using 32 [t]hreads and compress the result to save space:
+
+`bwa mem -t 32 {{path/to/reference.fa}} {{path/to/read_single_end.fq.gz}} | gzip > {{path/to/alignment_single_end.sam.gz}}`
+
+- Map pair-end reads (sequences) to the indexed genome using 32 [t]hreads and compress the result to save space:
+
+`bwa mem -t 32 {{path/to/reference.fa}} {{path/to/read_pair_end_1.fq.gz}} {{path/to/read_pair_end_2.fq.gz}} | gzip > {{path/to/alignment_pair_end.sam.gz}}`
+
+- Map pair-end reads (sequences) to the indexed genome using 32 [t]hreads with [m]arking shorter split hits as secondary for output SAM file compatibility in Picard software and compress the result:
+
+`bwa mem -M -t 32 {{path/to/reference.fa}} {{path/to/read_pair_end_1.fq.gz}} {{path/to/read_pair_end_2.fq.gz}} | gzip > {{path/to/alignment_pair_end.sam.gz}}`
+
+- Map pair-end reads (sequences) to indexed genome using 32 [t]hreads with FASTA/Q [c]omments (e.g. BC:Z:CGTAC) appending to a compressed result:
+
+`bwa mem -C -t 32 {{path/to/reference.fa}} {{path/to/read_pair_end_1.fq.gz}} {{path/to/read_pair_end_2.fq.gz}} | gzip > {{path/to/alignment_pair_end.sam.gz}}`