chore: update mpileup commands quality options

Author: ahmig

workflow/rules/vaf.smk

@@ -219,7 +219,7 @@ rule samtools_depth_all_sites:
     log:
         LOGDIR / "samtools_depth_all_sites" / "{sample}.txt",
     shell:
-        "samtools depth --threads {threads} -a -H -J -Q {params.min_mq} -q {params.min_bq} -o {output:q} {input:q} >{log:q} 2>&1"
+        "samtools depth --threads {threads} -a -H -J -Q {params.min_bq} -q {params.min_mq} -o {output:q} {input:q} >{log:q} 2>&1"
 
 
 rule bcftools_mpileup_all_sites:
@@ -238,7 +238,7 @@ rule bcftools_mpileup_all_sites:
         mpileup = LOGDIR / "bcftools_mpileup_all_sites" / "{sample}.mpileup.txt",
         query = LOGDIR / "bcftools_mpileup_all_sites" / "{sample}.query.txt",
     shell:
-        "bcftools mpileup --ignore-RG -a AD,ADF,ADR --fasta-ref {input.reference:q} --threads {threads} -Q {params.min_mq} -q {params.min_bq} -Ov -o {output.mpileup:q} {input.bam:q} >{log.mpileup:q} 2>&1 && "
+        "bcftools mpileup --no-BAQ -a AD,ADF,ADR --fasta-ref {input.reference:q} --threads {threads} -Q {params.min_bq} -q {params.min_mq} -Ov -o {output.mpileup:q} {input.bam:q} >{log.mpileup:q} 2>&1 && "
         "echo 'CHROM\tPOS\tREF\tALT\tDP\tAD\tADF\tADR' >{output.query:q} && "
         "bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%DP\t[ %AD]\t[ %ADF]\t[ %ADR]\n' {output.mpileup:q} >>{output.query:q} 2>{log.query:q}"