Changes between Version 29 and Version 30 of SOPs/variant_calling

Timestamp:

03/13/19 14:29:34 (6 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling

@@ -131 +131 @@
 }}}
 
-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]:
+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].   Note that you'll only get a maximum coverage of ~8000 reads unless you include location (ex: chr19:50-100) as the final argument for 'bam-readcount'.
 {{{
-bam-readcount -l Desired_sites.bed -f refGenome.fa Sample.bam > Desired_sites.nt_counts_etc.txt
+bam-readcount -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