Changes between Version 14 and Version 15 of SOPs/vcf_manipulation

Timestamp:

03/17/23 10:30:26 (3 years ago)

Author:

gbell

Comment:

--

SOPs/vcf_manipulation

@@ -99 +99 @@
 }}}
 
-Extract fields from a VCF file to a TXT, tab separated format with [http://snpeff.sourceforge.net/SnpSift.html#Extract snpSift extractFields] function
+Extract fields from a VCF file to a TXT, tab separated format with the [http://snpeff.sourceforge.net/SnpSift.html#Extract snpSift extractFields] function
 {{{
 # Extract chromosome, position, reference base(s), alternate bases(s), all the samples' ADF and ADR (number of high-quality ref-fwd, alt-fwd, ref-reverse, and alt-reverse bases):
@@ -107 +107 @@
 java -jar SnpSift.jar extractFields foo.vcf CHROM POS REF ALT "GEN[*].ADF[*]" "GEN[*].ADR[*]" > Foo.ADF.ADR.split.vcf
 }}}
+
+Extract fields from a VCF file to a TXT, tab separated file with the [https://samtools.github.io/bcftools/howtos/query.html bcftools query] function
+
+{{{
+# Extract any fields that are in the INFO or other fields
+bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%AC\t%AN\t%AF\n' gnomad.genomes.r2.1.1.sites.21.vcf.bgz > gnomad.genomes.r2.1.1.sites.21.vcf.AC+AN+AF.txt
+# Start by keeping only SNPs (so remove indels)
+bcftools view --types snps gnomad.genomes.r2.1.1.sites.21.vcf.bgz | bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%AC\t%AN\n' >| gnomad.genomes.r2.1.1.sites.21.vcf.SNPs_only.AC+AN+AF.txt
+# Make a bedgraph file using an output value (such as AF for the score)
+awk -F"\t" '{print "chr"$1 "\t" $2-1 "\t" $2 "\t" $7}' gnomad.genomes.r2.1.1.sites.21.vcf.AC+AN+AF.txt >| gnomad.genomes.r2.1.1.sites.21.AF.bedgraph
+# Make output a bed file showing the REF and ALT alleles (like "G>C" for QC)
+awk -F"\t" '{print "chr"$1 "\t" $2-1 "\t" $2 "\t" $3">"$4}' gnomad.genomes.r2.1.1.sites.21.vcf.AC+AN+AF.txt >| gnomad.genomes.r2.1.1.sites.21.bed
+}}}