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Bioconductor / Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
https://bioconductor.org/packages/Rsamtools
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min_nucleotide_depth parameter of PileupParam doesn't take 0 #19

Open sarahwajid opened 3 years ago

sarahwajid commented 3 years ago

Hello

If a user wants all positions output even if a reference position has zero coverage, the min_nucleotide_depth parameter=0 does not work to output the position with zero coverage.

p_param <- PileupParam(min_nucleotide_depth=0L,min_minor_allele_depth=0L,distinguish_strands=TRUE,min_mapq=10L,min_base_quality =10L,max_depth=200000L, distinguish_nucleotides=TRUE, ignore_query_Ns=FALSE,include_deletions=TRUE, include_insertions=TRUE)

ArjenB85 commented 3 years ago

I am struggling with the exact same problem! Did you solve it?