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# example script to test
full_86k_vcf=#***real file location deliberately obscured***
# example 1: not using reftable. 1 1827835 CTTGG CTGG $na12878_alone_all -i
# further examples using reftable against 86k dataset
# three ways to find the same variant 1 861223 AG CG $full_86k_vcf -t $reftable_86k -i # as found in reference VCF 1 861222 TAG TCG $full_86k_vcf -t $reftable_86k -i # a different non-minimal representation of same variant 1 861223 A C $full_86k_vcf -t $reftable_86k -i # searching for the minimal representation
# search for the other allele at the same site 1 861223 AG A $full_86k_vcf -t $reftable_86k -i
# three ways to find another variant 1 878677 CCT TCT $full_86k_vcf -t $reftable_86k -i # as found in reference VCF 1 878676 ACCT ATCT $full_86k_vcf -t $reftable_86k -i 1 878677 C T $full_86k_vcf -t $reftable_86k -i # searching for minimal representation
# and another 1 879058 T TC $full_86k_vcf -i
# also works on bi-allelic sites 1 878680 G T $full_86k_vcf -i
# test multi-variant mode
echo -e "1 861223 AG CG\n1 878677 CCT TCT" > variant_list.txt $full_86k_vcf -l variant_list.txt -t $reftable_86k -i
# or without returning individual-level variants $full_86k_vcf -l variant_list.txt -t $reftable_86k
# can also look up both alleles at a site if comma-separated in input
# (useful for grabbing lines directly from a VCF to look up) 1 861223 AG A,CG $full_86k_vcf -t $reftable_86k -i