List VCF¶

Command examples:¶

atav.sh --list-vcf --sample PATH_TO_SAMPLE_FILE --out PATH_TO_OUTPUT_DIR

Command options:¶

--list-vcf: trigger list vcf function.

All the Command Options are available to use in this function.

Output:¶

variants.vcf

##fileformat=VCFv4.2
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=ANN,Number=.,Type=String,Description="Consequence annotations: Effect|Gene|Transcript|HGVS_c|HGVS_p|Polyphen_Humdiv|Polyphen_Humvar">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
#CHROM  POS     ID      REF     ALT     QUAL     FILTER     INFO    FORMAT

Please check Output Columns for common columns.