How to call LOH with FreeC
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11 months ago
giusdalt95 ▴ 10

Good morning, I am try to infer loss of heterozygosity (LOH) from WGS data using Freec. For this purpose, I am using these parameters in the "[BAF]" section of the configuration file:

[BAF]

makePileup = My_somaticVCF.vcf.gz
fastaFile = hg19.fa
SNPfile = hg19_snp142.SingleDiNucl.1based.txt.gz

When I run the command to perform the analysis (freec -conf config.file.txt -sample myTumor.bam -control myNormal.bam) I get such error:

[opened FIFO for writing] /tmp/sambamba-pid4022492-efnu/5
[E::hts_open_format] Failed to open file "1" : No such file or directory
[mpileup] failed to open 1: No such file or directory
[executing] /srv/ngsdata/dalteriog/Tools/miniconda3/envs/ngspipe/bin/samtools mpileup /tmp/sambamba-pid4022492-efnu/6 -l /tmp/sambamba-pid4022492-efnu/6.bed -f /srv/ngs/analysis/dalteriog/reference_genomes/hs/hg19.fa -d 8000 -Q 0 1 -l ./chr21.SP_1_T.bam_SNPinNewCaptureRegions.bed| /srv/ngsdata/dalteriog/Tools/miniconda3/envs/ngspipe/bin/sambamba strip_bcf_header --vcf| /srv/ngsdata/dalteriog/Tools/miniconda3/envs/ngspipe/bin/sambamba lz4compress

I've looked up the web and the only answer that was a bit relatable to my question was that samtools mpileup has been deprecated, and it's recommended to use bcftools mpileup instead. Obviously, as you can figure out, I cannot change the aforementioned command, so I was asking myself if it's possible to infer LOH with FreeC from WGS data or have I to change tool. Thank you. Peppe

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