User: gsr9999

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gsr999990
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Posts by gsr9999

<prev • 31 results • page 1 of 4 • next >
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How to preserve Sample Identity within the metadata of FASTQ, BAM and VCF files; CAP AMP 2018 Guidelines - Recommendation 10
... Hi BioStar Leaders, In our lab, I have designed an exome pipeline based on BWA and GATK-HaplotypeCaller and it confirms to 2016/2017 guidelines from College of American Pathologists(CAP) and Association for Medical Pathology(AMP). Recently in 2018, the AMP-CAP published 2018 guidelines [here][1] ...
next-gen alignment sequencing written 11 weeks ago by gsr999990
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Comment: C: how to Automate the Retrieval of Variant-related Information from Pubmed, dbSNP,
... Thanks for ur ideas Kevin ...
written 11 weeks ago by gsr999990
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Comment: C: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover,
... Thanks for this summary list ...
written 6 months ago by gsr999990
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Answer: A: How to generate a .sam/.bam file of a particular chromosome or even a particular
... You can also use sambamba tool to slice the existing bam to specific regions. It is much faster than samtools. Example : $sambamba slice -o my_output_bam_file.bam Input_bam_file.bam chr1:100-200 Or you can extract reads for an entire chromosome by just specifying the chromosome name in option Exa ...
written 8 months ago by gsr999990
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Comment: C: question about API for SNPs
... thanks for this info on Ensemble Restful apis ...
written 9 months ago by gsr999990
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Comment: C: Searching for ClinVar entries based on SNP annotation
... thanks for the post and link ...
written 9 months ago by gsr999990
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how to Automate the Retrieval of Variant-related Information from Pubmed, dbSNP, ClinVar, HGMD etc
... Dear Biostar leaders, I have started to work on a new Variant Re-Classification project in my lab, and I am wondering how others implement this and it would be great if you could share/advice on best approaches being practiced. After sanger confirmation of WES variants, we classify variants based o ...
genome gene next-gen snp written 9 months ago by gsr999990 • updated 9 months ago by Kevin Blighe33k
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Comment: C: Can Breakdancer be applied on Paired end Exome Sequencing data for germline copy
... Hi Cameron, Thank you for the details/information on how breakdancer is best suited for short read sequencing <2*50 bp. Thank u for pointing me to other tools like lumpy, manta and gridss. ...
written 9 months ago by gsr999990
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Answer: A: Can Breakdancer be applied on Paired end Exome Sequencing data for germline copy
... After reading review papers, I learnt that CNV detection in Exome data by SV detection tools that are based on Discordant Read Pairs like Breakdancer may not be able to detect CNVs in every case. These tools require at least one breakpoint to be in exonic regions, and when real breakpoint is outside ...
written 9 months ago by gsr999990
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Comment: C: Recommendations for CNV calling algorithms/programs to benchmark
... Can Breakdancer be applied on Paired End Whole Exome sequencing data ? ...
written 9 months ago by gsr999990

Latest awards to gsr9999

Popular Question 20 months ago, created a question with more than 1,000 views. For BWA MEM 0.7.12 Error : [gzread] : invalid distance code
Scholar 21 months ago, created an answer that has been accepted. For A: Gcat Benchmarking Tool For Comparison Of Genome Analysis Software
Scholar 21 months ago, created an answer that has been accepted. For A: Gcat Benchmarking Tool For Comparison Of Genome Analysis Software

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