SNP calling from the GL field

[samtools.git] / bcftools / call1.c

diff --git a/bcftools/call1.c b/bcftools/call1.c
index 1060513cfb104072c271aee4646905351b06f99b..995d500eb69ad028a1b0ed2a75da5bde88d92bee 100644 (file)
--- a/bcftools/call1.c
+++ b/bcftools/call1.c
@@ -287,6 +287,7 @@ int bcfview(int argc, char *argv[])
                }
                if (vc.flag & VC_CALL) {
                        bcf_p1rst_t pr;
+                       bcf_gl2pl(h->n_smpl, b);
                        bcf_p1_cal(b, p1, &pr); // pr.g[3] is not calculated here
                        if (vc.flag&VC_HWE) bcf_p1_cal_g3(p1, pr.g);
                        if ((n_processed + 1) % 50000 == 0) bcf_p1_dump_afs(p1);