For annotating large variants, such as CNVs or structural variants (SVs), it can be useful to annotate theendsof the variant in addition to the region itself. To do this, specify the-endsflag tovcfanno. e.g.: vcfanno -ends example/conf.toml example/query.vcf.gz ...
VCF Annotation Tools is a python package that includes several tools to annotate VCF files with data from other tools. vcf-readcount-annotator A tool that will add the data from bam-readcount files to the VCF sample column. vcf-expression-annotator A tool that will add the data from several...
cl2 = ("vcfcat <({bcftools_cmd_chi2} {scalpel_tmp_file}) ""<({bcftools_cmd_common} {scalpel_tmp_file_common}) | "" {fix_ambig} | {vcfstreamsort} {compress_cmd} > {tx_out_file}") do.run(cl2.format(**locals()),"Finalising Scalpel variants", {}) ann_file = annotation....
I generated variant calls with bcftools and had no error messages. Then I ran bcftools csq and it also had no error messages and generated consequence.vcf files for each of the vcfs but bcftools csq did not annotate the consequenc.vcf fi...
vcf2tsvis an additional program in bcfanno package, use to convert VCF/BCF file to user-friendly tab-seperated-variants file. ./bcfanno -c toy.json example/toy.vcf.gz -q | ./vcf2tsv -f CHROM,POS,CytoBand,REF,ALT,GT,SAMPLE,RS,MolecularConsequence,Gene,HGVSnom,ExonIntron,AAlength,HGMD...
A fast and flexible program to annotate/interpret genetic variants in VCF/BCF file - shiquan/bcfanno