Changes between Version 27 and Version 28 of SOPs/variant_calling

Timestamp:

10/18/18 12:25:33 (6 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling

@@ -80 +80 @@
 }}}
 
+Summarize variant statistics for each sample (with 'bcftools stats') and plot them.
+{{{
+bcftools stats -F <ref.fa> -s - <results.vcf> > <results.vcf.stats.txt>
+plot-vcfstats -p vcfstats <results.vcf.stats.txt>
+}}}
+
 Prepare file of known SNPs for use with vcf-annotate.
 Start with tab-delimited file (ex: SNP137.bed) that looks like 
@@ -132 +138 @@
 }}}
 
+== Create a consensus sequence by applying VCF variants to a reference genome file ==
+
+{{{
+bgzip All_samples.variants.withTags.vcf
+tabix -p vcf All_samples.variants.withTags.vcf.gz
+samtools faidx Ref_genome.fa chr1:1-1000 | bcftools consensus All_samples.variants.withTags.vcf.gz > chr1_1_1000.consensus.fa
+}}}
 
 == Original page ==