[mpileup] no input file/data given in Estimating False Negative Rate

[AlejandroMS17]

Hi Adam,

I am trying to run the "bcftools mpileup" step to estimate the false negative rate, but I am getting this error

amorales@dacelo:/disks/dacelo/data/03_analyses_RB7_7_fa_as_reference_chapter_2_thesis/06_false_negative_rate_estimation/test_false_negative_rate$ bcftools mpileup -a 'AD,DP' -T RB7_7_fa_fai_sites_to_mutate.bed -q3 -Q13 -Ou -f RB7_7.fa | bcftools call -m -A -p 0 -P 0.015 -O z -o RB7_7_bcftools.vcf.gz Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] no input file/data given Failed to open -: unknown file type amorales@dacelo:/disks/dacelo/data/03_analyses_RB7_7_fa_as_reference_chapter_2_thesis/06_false_negative_rate_estimation/test_false_negative_rate$

Did you get this error too?

Do we need to provide a BAM file?
Usage: bcftools mpileup [options] in1.bam [in2.bam [...]]

Thank you!.

[adamjorr]

Yes, you should provide the bam file as input there. Thanks for reporting this, I'll fix it in the readme ASAP

[AlejandroMS17]

Great!, thanks for the prompt reply.

[AlejandroMS17]

One more question in regards of the BAM file as input file. Does the BAM file needs to contains all the samples?.

Because in the following step I got the following error:

amorales@dacelo:/disks/dacelo/data/03_analyses_RB7_7_fa_as_reference_chapter_2_thesis/06_false_negative_rate_estimation/test_false_negative_rate$ bcftools query -s GL/M -f '%CHROM\t%POS\t%REF\t%FIRST_ALT\t[%TGT]\n' RB7_7_bcftools.vcf.gz | tr '/' '\t' > RB7_7_fa_fai_sites_to_mutate.txt Sample name mismatch: sample #1 not found in the header

The input BAM file that I used for this test, did not contain all the samples.

I am guessing I need to provide that information in:

bcftools query -s GL/M

[adamjorr]

Yes, for that step you should pass the sample name of the root sample with the -s option.