calculate posterior allele frequency

[samtools.git] / bam_plcmd.c

diff --git a/bam_plcmd.c b/bam_plcmd.c
index 2afebeadf85bc2ee020e3c8aecd0209dccebc51d..258b83fd72b6ac21db863ea837d46c92d0ff0aef 100644 (file)
--- a/bam_plcmd.c
+++ b/bam_plcmd.c
@@ -521,6 +521,10 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                kstring_t s;
                s.l = s.m = 0; s.s = 0;
                puts("##fileformat=VCFv4.0");
+               puts("##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total read depth\">");
+               puts("##INFO=<ID=AF,Number=1,Type=Float,Description=\"Posterior non-reference allele frequency\">");
+               puts("##INFO=<ID=AFEM,Number=1,Type=Float,Description=\"Prior-free non-reference allele frequency by EM\">");
+               puts("##FILTER=<ID=Q13,Description=\"All min{baseQ,mapQ} below 13\">");
                kputs("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", &s);
                for (i = 0; i < n; ++i) {
                        const char *p;
@@ -549,12 +553,12 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                        ref_tid = tid;
                }
                if (conf->vcf) {
-                       double f0, f, pref = -1.0; // the reference allele frequency
+                       double f0, f, fpost, pref = -1.0; // the reference allele frequency
                        int j, _ref, _alt, _ref0, depth, rms_q, _ref0b, is_var = 0, qref = 0;
                        uint64_t sqr_sum;
                        _ref0 = _ref0b = (ref && pos < ref_len)? ref[pos] : 'N';
                        _ref0 = bam_nt16_nt4_table[bam_nt16_table[_ref0]];
-                       f = f0 = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
+                       f = f0 = fpost = mc_freq0(_ref0, n_plp, plp, ma, &_ref, &_alt);
                        if (f >= 0.0) {
                                double q, flast = f;
                                for (j = 0; j < 10; ++j) {
@@ -563,8 +567,10 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                                        if (fabs(f - flast) < 1e-3) break;
                                        flast = f;
                                }
-                               if (1. - f < 1e-4) f = 1.;
                                pref = mc_ref_prob(ma);
+                               fpost = mc_freq_post(ma);
+                               if (1. - f < 1e-4) f = 1.;
+                               if (1. - fpost < 1e-4) fpost = 1.;
                                is_var = (pref < .5);
                                q = is_var? pref : 1. - pref;
                                if (q < 1e-308) q = 1e-308;
@@ -589,13 +595,15 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
                                }
                        }
                        rms_q = (int)(sqrt((double)sqr_sum / depth) + .499);
-                       printf("DP=%d;MQ=%d;AF=%.3lg", depth, rms_q, f0<0.?0.:1.-f);
-                       printf("\tGT:GQ:DP");
-                       // output genotype information; FIXME: to be implmented...
-                       for (i = 0; i < n; ++i) {
-                               int x = mc_call_gt(ma, f, i);
-                               printf("\t%c/%c:%d:%d", "10"[((x&3)==2)], "10"[((x&3)>0)], x>>2, n_plp[i]);
-                       }
+                       printf("DP=%d;MQ=%d", depth, rms_q);
+                       if (fpost >= 0. && fpost <= 1.) printf(";AF=%.3lg", 1. - fpost);
+                       if (f >= 0. && f <= 1.) printf(";AFEM=%.3lg", 1. - f);
+                       if (fpost >= 0. && fpost <= 1.) {
+                               for (i = 0; i < n; ++i) {
+                                       int x = mc_call_gt(ma, fpost, i);
+                                       printf("\t%c/%c:%d:%d", "10"[((x&3)==2)], "10"[((x&3)>0)], x>>2, n_plp[i]);
+                               }
+                       } else for (i = 0; i < n; ++i) printf("\t./.:0:0");
                        putchar('\n');
                } else {
                        printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');