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Since most of the work is in setting up the necessary tools and pipelines to evaluate, I will lump the actual act of evaluating on specific data into this single ticket. We need to:
* CRSP specifi…
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when I run the following command
./CnvHunter -in xxx/S003_cfdna_depth.tsv xxx/S010_gdna_depth.tsv -out xx/cnvhunter.tsv ,
i always get the following excepthion,
Exception: At least n+1 input files…
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We could save a lot of time in PairHMM if we could identify reads supporting the reference allele and run PairHMM only on reads supporting alt alleles and a random sample of ref reads. This could esp…
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- [x] [data format] decide whether a mutation is called or uncalled mutation in MAF -- check the current MAF to see if there is indication about uncalled events, if not, contact Nick.
- [x] [database…
jjgao updated
7 years ago
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Hi,
I see in your paper for the second time you pass through the Poisson cdf, you use a value of N/2. However, I do not see that reflected in your code, so I was wondering how you implemented that…
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For example, the following maf input gives the wrong vcf output
```
Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classifi…
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I encounter InexactError when reading BAM files
```
ERROR: InexactError()
in readbytes!(::Libz.Source{:inflate,BufferedStreams.BufferedInputStream{IOStream}}, ::Array{UInt8,1}, ::Int64, ::Int64)…
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Our contamination downsampling code is somewhat intelligent. `AlleleBiasedDownsamplingUtils` contains methods to downsample the most suspicious reads up to a given contamination fraction. However, i…
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I ran `GetBayesianHetCoverage` on some normal ICE exomes today and got a NullPointerException on one of the samples.
**Call**
```
java -Xmx9g -Djava.library.path=/broad/software/free/Linux/redhat_6_…