SeungJin Park
SeungJin Park
Hi, I am trying to build an index. but I got the following error: `exceeded integer bounds, remove adjacent SNPs, use haplotypes, or switch to a large index (--large-index).` but...
`# hap.py NA12878.vcf.gz 01.Raw_variants.vcf.gz -f ConfidentRegions.bed.gz -o test -r hg38.fa ` ``` [I] Total VCF records: 4167900 [I] Non-reference VCF records: 4167900 [W] overlapping records at chr1:37070742 for sample 0...
I got error below. How could I do that? ``` python ena-fast-download.py ERR962744 03/12/2021 02:27:29 PM INFO: Using aspera ssh key file: $HOME/.aspera/connect/etc/asperaweb_id_dsa.openssh 03/12/2021 02:27:29 PM INFO: Querying ENA for...
/addData01/01_Program_to_install/75.MuSIC2/joinx/joinx/build/vendor/src/gtest160/include/gtest/gtest.h:269:3: note: no known conversion for argument 1 from ‘std::basic_istream’ to ‘const testing::AssertionResult&’ make[2]: *** [build/test/lib/fileformats/CMakeFiles/TestFileFormats.dir/build.make:206: build/test/lib/fileformats/CMakeFiles/TestFileFormats.dir/TestVcfEntry.cpp.o] error 1 make[1]: *** [CMakeFiles/Makefile2:357: build/test/lib/fileformats/CMakeFiles/TestFileFormats.dir/all] error 2 make: *** [Makefile:163: all] error...
at directory of samtools1.9 # export SAMDIR=$PWD # cd ../calcRoiCovg/ # make Please define environment variable SAMDIR to point to your samtools libraries what should I do that? Thanks
root@sever:MUSIC2# music2 smg --gene-mr-file result/gene_mrs --output-file smgs --max-fdr 0.05 --processors 1 Error in read.table(file = file, header = header, sep = sep, quote = quote, : more columns than column...
I got error below. Can you help me out? Thanks. ``` python `which 2020plus.py` features -s output_bladder/simulated_summary/chasm_sim_summary2.txt --tsg-test output_bladder/simulated_summary/tsg_sim2.txt -og-test output_bladder/simulated_summary/oncogene_sim2.txt -o output_bladder/simulated_summary/simulated_features2.txt python: can't open file 'features': [Errno 2]...
Dear Karchin I have maf file from aligning grch38 ver. Can I get a hg38 'snvboxgene.bed' from you? Thanks.
Dear developer. I am working on measuring the performance of vg using Illumina Platinum Genome data. Compared to hisat2, it was confirmed that indel precision in vg was too low....
"Whole-genome sequencing and targeted amplicon capture" says: > "Do not mark duplicates in the BAM files for samples sequenced by this method" However, in the BAM file preparation, it is...