fix VAF

yangao07 · yangao07 · commit 6a64fc7cf81b · 2026-04-06T21:10:59.000+08:00
diff --git a/src/vcf_utils.c b/src/vcf_utils.c
@@ -218,10 +218,10 @@ int write_var_to_vcf(var_t *vars, const struct call_var_opt_t *opt, bam_chunk_t
             len += snprintf(buffer + len, buf_m - len, "%d", var.AD[j]);
         }
         // VAF
-        for (int j = 0; j < 1 + var.n_alt_allele; j++) {
+        for (int j = 0; j < var.n_alt_allele; j++) {
             if (j == 0) len += snprintf(buffer + len, buf_m - len, ":");
             if (j > 0) len += snprintf(buffer + len, buf_m - len, ",");
-            float vaf = (float)var.AD[j] / var.DP;
+            float vaf = (float)var.AD[j+1] / var.DP;
             len += snprintf(buffer + len, buf_m - len, "%.3f", vaf);
         }
         // GQ

Original file line number	Diff line number	Diff line change
`@@ -218,10 +218,10 @@ int write_var_to_vcf(var_t vars, const struct call_var_opt_t opt, bam_chunk_t`
`218`	`218`	`len += snprintf(buffer + len, buf_m - len, "%d", var.AD[j]);`
`219`	`219`	`}`
`220`	`220`	`// VAF`
`221`		`- for (int j = 0; j < 1 + var.n_alt_allele; j++) {`
	`221`	`+ for (int j = 0; j < var.n_alt_allele; j++) {`
`222`	`222`	`if (j == 0) len += snprintf(buffer + len, buf_m - len, ":");`
`223`	`223`	`if (j > 0) len += snprintf(buffer + len, buf_m - len, ",");`
`224`		`- float vaf = (float)var.AD[j] / var.DP;`
	`224`	`+ float vaf = (float)var.AD[j+1] / var.DP;`
`225`	`225`	`len += snprintf(buffer + len, buf_m - len, "%.3f", vaf);`
`226`	`226`	`}`
`227`	`227`	`// GQ`