Changes between Version 23 and Version 24 of SOPs/variant_calling

Timestamp:

08/25/17 15:05:00 (7 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling

@@ -127 +127 @@
 If you want counts for all 4 nucleotides (not just reference and alternate alleles), one way is with [https://github.com/genome/bam-readcount bam-readcount]:
 {{{
-bam-readcount -l Desired_sites.bed -f refGenome.fa Sample.bam > Desired_sites.nt_counts.txt
+bam-readcount -l Desired_sites.bed -f refGenome.fa Sample.bam > Desired_sites.nt_counts_etc.txt
+# Extract just nt counts (fields: chr, position, reference_base, depth, As, Cs, Gs, Ts)
+perl -pe 's/:/\t/g' | cut -f1-4,20,34,48,62 Desired_sites.nt_counts_etc.txt > Desired_sites.nt_counts_only.txt
 }}}