if (em[5] >= 0 && em[6] >= 0) ksprintf(&s, ";AF2=%.4g,%.4g", 1 - em[5], 1 - em[6]);
if (em[7] >= 0) ksprintf(&s, ";LRT=%.3g", em[7]);
if (em[8] >= 0) ksprintf(&s, ";LRT2=%.3g", em[8]);
- //if (em[9] >= 0) ksprintf(&s, ";LRT1=%.3g", em[9]);
}
if (cons_llr > 0) {
ksprintf(&s, ";CLR=%d", cons_llr);
kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=RP,"))
kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=VDB,"))
+ kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=GT,"))
kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
if (!strstr(str.s, "##FORMAT=<ID=SP,"))
kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=PL,"))
- kputs("##FORMAT=<ID=PL,Number=-1,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2\">\n", &str);
+ kputs("##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">\n", &str);
h->l_txt = str.l + 1; h->txt = str.s;
}
if (!(l > begin && end > b->pos)) continue;
}
++n_processed;
- if (vc.flag & VC_QCNT) { // summarize the difference
+ if ((vc.flag & VC_QCNT) && !is_indel) { // summarize the difference
int x = bcf_min_diff(b);
if (x > 255) x = 255;
if (x >= 0) ++qcnt[x];