rptashkin / facets2n Goto Github PK

Hello,

I generated the normal snp and then the loess.txt using 47 normal bams successfully using:

/usr/local/lib/R/site-library/facets2n/extcode/snp-pileup-wrapper.R --output-prefix /media/user/Seagate_Exome67_133/LIGUE/Exomes_67_133/FACETS/Tonly/standard_normals_cv3heme \ --vcf-file /media/user/Seagate_Exome67_133/LIGUE/Reference_files_WESpipeline/00-common_all.vcf.gz \ --unmatched-normal-BAMS "/media/user/Seagate_Exome67_133/LIGUE/Exomes_67_133/Alignments/Final_bams/*N_cleaned_bqsr.bam"
And then in R I created the loess object and try to load a snpMatrix (from a Tumor-normalUnmatched sample):

facets2n::MakeLoessObject(pileup = PreProcSnpPileup(filename = "/media/user/Seagate_Exome67_133/LIGUE/Exomes_67_133/FACETS/Tonly/standard_normals_cv3heme.snp_pileup.gz", is.Reference = TRUE,gbuild="hg38"), write.loess = TRUE, outfilepath = "/media/user/Seagate_Exome67_133/LIGUE/Exomes_67_133/FACETS/Tonly/standard_normals_cv3heme.loess.txt", is.Reference = TRUE,gbuild = "hg38") readu <- facets2n::readSnpMatrix(filename ="CNSL047T_CNSL005N.snp_pileup.gz", MandUnormal = TRUE, ReferencePileupFile = "/media/user/Seagate_Exome67_133/LIGUE/Exomes_67_133/FACETS/Tonly/standard_normals_cv3heme.snp_pileup.gz", ReferenceLoessFile = "/media/user/Seagate_Exome67_133/LIGUE/Exomes_67_133/FACETS/Tonly/standard_normals_cv3heme.loess.txt", useMatchedX = FALSE, refX=TRUE,gbuild = "hg38")

I got the following error:
imputed patient sex from matched normal: Female
Best normal for autosomes: NA
Best normal for ChrX: NA

Error in [.data.frame(combined.pileup, , best_normX) :
undefined columns selected
In addition: There were 50 or more warnings (use warnings() to see the first 50)

I tried lowering the "MinOverlap" to 0.75 but the error persists with this and other samples

Any suggestions or ideas to make it work?

Thanks in advance

unmatched-normal-BAMS "<some/path>/PoolNormal.bam"

can first check for at least one unmatched normal before this block

Which tools can create PoolNormal.bam, samtools merge?

unmatched-normal-BAMS "<some/path>/PoolNormal.bam"