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Hi, Markus and PureCN devs! Could use some help getting around a new bug.
So I'm trying to run PureCN for a tumor sample without a matched normal. My VCF comes from Mutect2 and I am using a proc…
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Code:
vcf1=Lumpy.vcf
vcf2=Delly.vcf
vcf3=Manta.vcf
$SurvivorPath/survivor_ant \
> -o combined.vcf \
> -l 20 \
> -v $vcf3 $vcf2 $vcf1 \
> -i $vcf1 \
> -b $hg19_geneANT
Output: PARSE ERR…
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testbam=/bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/SecondPanel/0_Illumina_UMI_Error_Corrected_bam/Sample1.collapsed.bam
out=/bgfs/soesterreich/pan_data/so…
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20:22:55.968 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/bgfs/soesterreich/pan_data/soesterreich/Tendo/InstalledTools/gridss/gridss.jar!/com/intel/gkl/native/libgkl_compre…
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Hi Sigve,
Please guide me, since I am getting below error:
docker run --rm -t -u 0 -v=/DATA/geyunxia/software/PCGR/pcgr.v0.7.0/pcgr-0.7.0:/data -v=/DATA/geyunxia/software/PCGR/pcgr.v0.7.0/pcgr-0.7.0…
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Hi!
I got the same warning as in issue #97.
I have a pair-end, not mate-pair, library, trimmed with skewer and aligned with bwa-mem. All my reads are from the same read-group so removing them is no…
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We've recently released MSK-ACCESS (cfDNA) data into the portal. Unlike existing clinical bioinformatic assays, very low VAF mutations will be reported with ACCESS. Currently, some ACCESS samples are…
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Hi Guys,
I am using smoove recently on targeted DNAseq files.
My code:
smoove call -x \
--name Lumpy \
--outdir $out \
--exclude $ExcludeBed \
--fasta $hg19_fasta \
-p 1 \
--genotype $t…
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This is my config file:
`details:
- algorithm:
tools_off:
- tumoronly-prioritization
- gemini
- coverage_qc
aligner: bwa
trim_reads: true
mark_duplicates: …
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Hi,i'm using facets on cfDNA sample(not FFPE),and i found the purity is NA,so i'm wondering whether facets can use on this situation?
thanks a lot.