how to create poolNormal bam? smatools merge?

[1512474508]

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

[rptashkin]

please refer to #20. do you have any other questions or issue with this parameter?

[1512474508]

Thanks!
If I have 6 samples，I would like to get sample1_tumor.bam' snp-pileup results and run facets2n. The code as below:
inst/extcode/snp-pileup-wrapper.R
-O pooledSample1
-vcf sample1.vcf
-n sample2_normal.bam (It's right? unmatched normal bam)
-t sample1_tumor.bam
-un "sample3_normal.bam sample4_normal.bam sample5_normal.bam sample6_normal.bam" (not using poolNormal bam, It's right?)

     readu <- readSnpMatrix(
                    filename = "./pooledSample1.snp-pileup.gz",
                    MandUnormal = TRUE,
                    useMatchedX = FALSE)

     It's right?

[1512474508]

or run the code:
snp-pileup -g -p -A -d 20000 -r 10,0,10,10,10,10
-q 0 -Q 0 -v sample1.vcf pooledsample1.snp-pileup.gz
sample2_normal.bam sample1_tumor.bam <path_to_assay_specific_unmatched_diploid_normals>/*bam

But the result is not good. I'm confused how to use the unmatched samples.

[rptashkin]

I think you have a few issues with the way you are using this tool:

1. The VCF used. The VCF should not be variant calls for a given tumor sample, but rather, a VCF of genome wide SNPs. You can download one for human genome here: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/00-common_all.vcf.gz

2. FACETS requires a matched normal for each tumor that you are trying to analyze. Unmatched normals will help with log ratio normalization, but are optional.

Please refer to the snp-pileup example in the README:

inst/extcode/snp-pileup-wrapper.R \ --snp-pileup-path <optional, path to snp-pileup executable, defaults to snp-pileup in your PATH> \ --vcf-file <path to SNP VCF> \ --normal-bam normal.bam \ --tumor-bam tumor.bam \ --output-prefix <prefix for output file, preferrably tumorSample__normalSample> --unmatched-normal-BAMS <if using unmatched BAMs for logR normalization, e.g. "<some/path/>*-N.bam" >

[rptashkin]

closing if no other questions