Changes between Version 11 and Version 12 of SOPs/variant_calling

Timestamp:

09/29/15 16:11:19 (10 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling

@@ -107 +107 @@
 See [wiki:SOPs/vcf Interpreting VCF files ] for more information.
 
+== Get read counts and statistics at desired sites ==
+
+Sometimes one may have an interesting set of genome locations that may not turn up in a variant output file (if they are variants in that sample, for example).
+
+If you need variant-type metrics for those sites, you can use a command like
+
+{{{
+samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -l Desired_sites.bed -f refGenome.fa Sample.bam | bcftools call -c - > Desired_sites_info.vcf 
+}}}
+
+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
+}}}
+
+
 == Original page ==