Changes between Version 1 and Version 2 of SOPs/vcf_manipulation

Timestamp:

10/16/13 10:18:05 (11 years ago)

Author:

gbell

Comment:

--

SOPs/vcf_manipulation

@@ -1 +1 @@
 = Manipulating VCF files = 
+
+Create a VCF ([http://en.wikipedia.org/wiki/Variant_Call_Format variant call format]) file [with about any program that identifies variants], such as
+* samtools' mpileup+bcftools: 
+{{{
+samtools mpileup -uf indexed_genome My_mapped_reads.bam | bcftools view -bvcg - >| My_mapped_reads.raw.bcf
+samtools mpileup -uf indexed_genome *.bam | bcftools view -bvcg - >| Multiple_samples.raw.bcf
+}}}
+
+Convert from BCF (binary version of VCF) to VCF:
+{{{
+bcftools view My_mapped_reads.raw.bcf > My_mapped_reads.raw.vcf
+}}}
+
+Convert from VCF to BCF:
+{{{
+bcftools view -bS -D chr_list.txt My_mapped_reads.raw.vcf > My_mapped_reads.raw.bcf
+}}}
+
+Merge multiple VCF files -- works on raw VCF files but apparently not with those processed by vcf-annotate
+
+{{{
+# For each VCF file:
+bgzip Variants_sample_A.raw.vcf
+tabix -p vcf Variants_sample_A.raw.vcf.gz
+}}}
+Merge multiple bgzipped, tabixed files:
+{{{
+vcf-merge *.raw.vcf.gz >| Variants_all_samples.raw.vcf
+}}}
+
+Annotate a VCF file (applying all filters with default values):
+{{{
+cat Variants_all_samples.raw.vcf | vcf-annotate -f + > Variants_all_samples.withTags.vcf
+}}}
+