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atks
A tool set for short variant discovery in genetic sequence data.
Greetings, we have a number of VCF files generated by non-MNV aware callers, but that do include phased genotypes and phase sets. Does (or can) Vt include a utility to...
Could peek subcommand list the type of every variants not just a summary text? Besides, I installed the lastest version vt, but the peek shows no -o parameter: > $...
installed OpenSSL 3.0, has the libcrypto.so.3 in /usr/bin, also copy it in /usr/local/bin. still had this problem while make test.
Been over 100 commits since 0.5772 - would be great to update the brew/conda packages.
Is there any way to limit the amount of memory vt norm uses? Currently I'm trying to remove the info fields from a massive vcf (>150GB) and the process just...
Hi, I have used your nice tool for a long time, downloading and installing within a Dockerfile. It has worked perfect for my purposes (multiallelic variant decomposition). However, I am...
Hello, I have the following deletion detected by Platypus, VarScan, GATK as: chr11 6411930 . C**CTGGTGCTGGCG** C Then I have the same one detected by SAMtools/bcftools as: chr11 6411930 ....
Please consider applying these three patches from new Debian package. https://salsa.debian.org/med-team/vt/-/tree/8d7a6047a9b5ecb846da38a0175ec394758eef8c/debian/patches * makefile: Get rid of external sources and update to libhts-1.10 * fix-spelling: Spelling fix * test-fail-on-error: Correct exit...
Deleted the reference index file. Downloaded reference genome from the UCSC database. But still getting the same error. vt normalize HF.final.vcf.gz -r ref/hg19.fasta -o normalizeHF.final.vcf.gz [variant_manip.cpp:72 is_not_ref_consistent] failure to extract...
Hi there I was running an older script which previously worked, but now threw an error at the step when I use vt sort on a VCF file: vt sort...
