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Dear Delly team,
Good evening.
In the output vcf file,
Alt showed without the insertion sequen…
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The normal result has 9 columns, the last two columns are not in my result!
version 11.6
`[general]
BedGraphOutput = FALSE
breakPointType = 2
chrFiles = /mnt/database/WES/b37/byChr
chrLenFile = …
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perl vcf2maf.pl --input-vcf /path/to/somaticvariants.vcf --output-maf /path/to/out.maf --tumor-id s_MC7562_tumor --normal-id s_MC7562_germline --vep-path /path/to/vep/94/ --vep-data /path/to/vep91/cac…
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Dear
I newly using dragmap as aligner for illumina sequenced fastq files using command:
/app/Genome/dragmap-1.2/bin/dragen-os -r ../.. /recalset/ -1 Output_Germline_Aziz/${i}_L001_R1_001.trim.fa…
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**Describe the bug**
Cancer caller hangs in a reproducible manner. The caller is started with 24 threads. Slowly the number of active threads appears to dwindle as I can see the CPU usage go down. …
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AB -> embryonic founder cell AB
EMS -> embryonic founder cell EMS -> should the definition of EMS be changed from ‘Embryonic cell’ to ‘Embryonic founder cell’? See WormAtlas founder cell definition.
…
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**Describe the bug**
Can't save h5mu from Scirpy processed gex+bcr+tcr data if I copy airr into obs (i.e. `tdata.obs = tdata.obs.join(ir.get.airr(tdata, tdata.obsm['airr'].fields))`).
Unlike in #4…
Ngort updated
2 months ago
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Hello,
I would like create a dataset for benchmark somatic variant caller with your software. Thanks for this clear documentation and your well-designed tool ! I just don't fully understand the gen…
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metrics calculated for each cell analyzed
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Hello:
I am using this library to read a VCF file that has been filtered (GATK Mutect2 + FilterMutectCalls) such as:
> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT LH0…