Changes between Version 42 and Version 43 of SOPs/miningSAMBAM

Timestamp:

02/07/20 10:27:55 (5 years ago)

Author:

gbell

Comment:

--

SOPs/miningSAMBAM

@@ -204 +204 @@
 bcftools call -O v -c Mapped_reads.variants.bcf | vcfutils.pl vcf2fq -d 2 >| Mapped_reads.consensus.fq
 }}}
+
+=== Convert BAM to BED format ===
+
+This can be helpful for genome browser viewing, as features in a BAM file are only visible when the browser is zoomed in enough, whereas BED features are visible at any scale.
+
+{{{
+# Use bam2bed from the bedtools suite
+# Run 'bam2bed -h' to get all options
+bam2bed < Mapped_reads.bam > Mapped_reads.bam
+}}}