SnpSift issues

can snpsift rename the INFO/TAG？

Hi，i use the snpsift to annotate the vcf file ,it's very useful ;but i found that the same INFO/TAG in both anno.vcf and input.vcf，such as: a.vcf INFO= b.vcf INFO= i...

litun-fkby

SnpSift split outputs only the first chromosome

6

Hi, I have a 3.8Gb VCF file produced by a WGS pipeline mapping on hg38 and mutation calling using Mutect2. The file contains chromosomes chr1 ... chr22, chrX, chrY and...

kmavrommatis

Adding alphamissense and other annotations from the latest dbNSFP

The latest dbNSFP includes annotations for AlphaMissense and other things that did not exist before. However, if I download the latest dbNSFP, build it, and then use it to annotate:...

ramirobarrantes

pom.xml: change repository url to https

hadoop-bam and typesafe repo url were using http preventing maven from downloading sources

kbipinkumar

Bump htsjdk from 2.24.1 to 3.0.1

Bumps [htsjdk](https://github.com/samtools/htsjdk) from 2.24.1 to 3.0.1. Release notes Sourced from htsjdk's releases. 3.0.1 Fix for a long standing vulnerability around temporary directory creation which could expose data to malicious users...

dependabot[bot]

dependencies

how to filter based on FREQ?

After annating by snpsift, how culd I filter based on FREQ? For example, a record with the following annotation, and I would like to filter based on GnomAD. How should...

chunxuan-hs

extract "ANN[*].RANK" from the ANN field

Hi, I have a vcf file annotated by snpeff and want to extract "ANN[*].RANK" from the ANN field like ANN=G|missense_variant|MODERATE|TNN|ENSG00000120332|transcript|ENST00000239462|protein_coding|13/19|c.3038C>G|p.Thr1013Arg|3151/5008|3038/3900|1013/1299|| java -jar /home/pmi/src/snpEff/SnpSift.jar extractFields my.vcf CHROM POS ID REF ALT...

gcy0115