Changes between Version 33 and Version 34 of SOPs/variant_calling

Timestamp:

09/02/20 16:29:31 (4 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling

@@ -142 +142 @@
 }}}
 
-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'.
+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'.  The file of coordinates of your desired sites must include chr, start, end but also be 1-based (so not bed format).
 {{{
-bam-readcount -w 1 -l Desired_sites.bed -f refGenome.fa Sample.bam chr1 > Desired_sites.nt_counts_etc.txt
+bam-readcount -w 1 -l Desired_sites.txt -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' Desired_sites.nt_counts_etc.txt | cut -f1-4,20,34,48,62 > Desired_sites.nt_counts_only.txt