Shruti Paniwala
A Bioinformatician
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A-allele of SLC24A5 gene is found to be responsible for variation in skin color of South-East...
By Rahul Agarwal 4061 days agoMore is the A -allele, More is fairer the Skin !!Variant Calling Pipeline
By LEGE 68 days agogithub.com - The variantcalling.nf nextflow script will take any number of samples with paired-end reads in FASTQ format, map reads using Bowtie2, process BAM files, and finally call variants using BCFtools v1.21 and/or Freebayes v1.3.6. If part of the...The Genome 10K Project
By Jit 3803 days agohttps://genome10k.soe.ucsc.edu The Genome 10K project aims to assemble a genomic zoo—a collection of DNA sequences representing the genomes of 10,000 vertebrate species, approximately one for every vertebrate genus. The trajectory of cost reduction...Variant Calling Resequencing-Based Genome Inference
By Abhi 148 days agoevomics.org - Variant Calling - Resequencing-Based Genome Inference Erik GarrisonUniversity of Tennessee Health Science CenterWorkshop on Genomics - Český KrumlovJanuary 12,...geck: trio-based comparative benchmarking of variant calls
By Jit 2047 days agogithub.com - Determine the accuracy of our model by comparing the precision and recall of GATK Unified Genotyper and Haplotype Caller on the high-confidence SNPs of the NIST Ashkenazim trio and the two independent Platinum Genome trios. We show that our method...Minda: a tool for evaluating structural variant (SV) callers
By LEGE 270 days agogithub.com - Minda is a tool for evaluating structural variant (SV) callers that standardizes VCF records for compatibility with both germline and somatic SV callers, benchmarks against a single VCF input file, or benchmarks against an ensemble call set...cisMuton: caller that detects SNVs/indels by comparing target (foreground) and control (background)...
By Jit 1780 days agostatic.ciscall.org - cisMuton is a caller that detects SNVs/indels by comparing target (foreground) and control (background) samples. cisMuton calls mutations from target capture regions, which are defined by the overlapping regions...Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
By Rahul Nayak 2600 days agogithub.com - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq dataAfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good...MinION_GC: An R script to do some QC on MinION data
By Radha Agarkar 2580 days agogithub.com - Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out...NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2334 days agogithub.com - NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...
