Changes between Version 32 and Version 33 of SOPs/variant_calling

Timestamp:

10/23/19 13:30:21 (5 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling

@@ -146 +146 @@
 bam-readcount -w 1 -l Desired_sites.bed -f refGenome.fa Sample.bam chr1 > 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
+perl -pe 's/:/\t/g' Desired_sites.nt_counts_etc.txt | cut -f1-4,20,34,48,62 > Desired_sites.nt_counts_only.txt
 }}}