cont

workflow.mk

@@ -25,7 +25,7 @@ result.vcf.gz: result.bcf
 	bcftools call  --multiallelic-caller --variants-only --output-type z -o $@ --format-fields GQ,GP $< 
 
 result.bcf : $(addsuffix .bam.bai,child father mother) $(addsuffix .bam,child father mother) ref.fa.fai
-	samtools mpileup -g --uncompressed --output-tags DP --fasta-ref ref.fa --output  $@ $(filter %.bam,$^)
+	bcftools mpileup -g --uncompressed --output-tags DP --fasta-ref ref.fa --output  $@ $(filter %.bam,$^)
 	
 
 $(eval $(call mapreads,father))