- fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
- fprintf(stderr, "Options: -c SNP calling\n");
- fprintf(stderr, " -v output potential variant sites only (force -c)\n");
- fprintf(stderr, " -g call genotypes at variant sites (force -c)\n");
- fprintf(stderr, " -b output BCF instead of VCF\n");
- fprintf(stderr, " -u uncompressed BCF output (force -b)\n");
- fprintf(stderr, " -S input is VCF\n");
- fprintf(stderr, " -A keep all possible alternate alleles at variant sites\n");
- fprintf(stderr, " -G suppress all individual genotype information\n");
- fprintf(stderr, " -H perform Hardy-Weinberg test (slower)\n");
- fprintf(stderr, " -N skip sites where REF is not A/C/G/T\n");
- fprintf(stderr, " -Q output the QCALL likelihood format\n");
- fprintf(stderr, " -L calculate LD for adjacent sites\n");
- fprintf(stderr, " -I skip indels\n");
- fprintf(stderr, " -1 INT number of group-1 samples [0]\n");
- fprintf(stderr, " -l FILE list of sites to output [all sites]\n");
- fprintf(stderr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta);
- fprintf(stderr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
- fprintf(stderr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
- fprintf(stderr, " -P STR type of prior: full, cond2, flat [full]\n");
+ fprintf(stderr, "Usage: bcftools view [options] <in.bcf> [reg]\n\n");
+ fprintf(stderr, "Input/output options:\n\n");
+ fprintf(stderr, " -A keep all possible alternate alleles at variant sites\n");
+ fprintf(stderr, " -b output BCF instead of VCF\n");
+ fprintf(stderr, " -D FILE sequence dictionary for VCF->BCF conversion [null]\n");
+ fprintf(stderr, " -F PL generated by r921 or before (which generate old ordering)\n");
+ fprintf(stderr, " -G suppress all individual genotype information\n");
+ fprintf(stderr, " -l FILE list of sites (chr pos) or regions (BED) to output [all sites]\n");
+ fprintf(stderr, " -L calculate LD for adjacent sites\n");
+ fprintf(stderr, " -N skip sites where REF is not A/C/G/T\n");
+ fprintf(stderr, " -Q output the QCALL likelihood format\n");
+ fprintf(stderr, " -s FILE list of samples to use [all samples]\n");
+ fprintf(stderr, " -S input is VCF\n");
+ fprintf(stderr, " -u uncompressed BCF output (force -b)\n");
+ fprintf(stderr, "\nConsensus/variant calling options:\n\n");
+ fprintf(stderr, " -c SNP calling (force -e)\n");
+ fprintf(stderr, " -d FLOAT skip loci where less than FLOAT fraction of samples covered [0]\n");
+ fprintf(stderr, " -e likelihood based analyses\n");
+ fprintf(stderr, " -g call genotypes at variant sites (force -c)\n");
+ fprintf(stderr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
+ fprintf(stderr, " -I skip indels\n");
+ fprintf(stderr, " -m FLOAT alternative model for multiallelic and rare-variant calling, include if P(chi^2)>=FLOAT\n");
+ fprintf(stderr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
+ fprintf(stderr, " -P STR type of prior: full, cond2, flat [full]\n");
+ fprintf(stderr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta);
+ fprintf(stderr, " -T STR constrained calling; STR can be: pair, trioauto, trioxd and trioxs (see manual) [null]\n");
+ fprintf(stderr, " -v output potential variant sites only (force -c)\n");
+ fprintf(stderr, "\nContrast calling and association test options:\n\n");
+ fprintf(stderr, " -1 INT number of group-1 samples [0]\n");
+ fprintf(stderr, " -C FLOAT posterior constrast for LRT<FLOAT and P(ref|D)<0.5 [%g]\n", vc.min_lrt);
+ fprintf(stderr, " -U INT number of permutations for association testing (effective with -1) [0]\n");
+ fprintf(stderr, " -X FLOAT only perform permutations for P(chi^2)<FLOAT [%g]\n", vc.min_perm_p);