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Pipeline using facets for fraction and copy number estimate from tumor/normal sequencing

License: GNU General Public License v3.0

Dockerfile 3.86% Shell 2.60% Nextflow 70.39% R 23.14%

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adigenova avatar mfoll avatar nalcala avatar tdelhomme avatar v-catherine avatar

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nalcala

facets-nf's Issues

NA purity

Thanks for your very helpful pipeline. I am just wondering why there are some NA values in purity (their ploidy are 2)...Here is my code:

nextflow run /home/kangwang/facets-nf/facets-nf/main.nf -profile singularity\
 --cohort_dir "/home/kangwang/facets-nf/data/Baseline" \
 --tn_file "/home/kangwang/facets-nf/data/TN_baseline.txt" \
 -with-singularity /home/kangwang/facets-nf/facets-suite_IARC.img --ref hg38  \
 --dbsnp_vcf_ref /home/kangwang/facets-nf/ref/00-common_all.vcf.gz \
 --analysis_type exome \
 --suffix_tumor "" --suffix_normal "" \
 -resume

Can I refine it by changing some parameters?

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