User: mdm-two

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mdm-two200
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Posts by mdm-two

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Tools For Structural Variants
... You don't say if you are looking for somatic or germline SVs, nor if you are calling in populations or individuals. Squaredancer and CREST use clipped reads whereas Breakdancer uses mapped reads pairs. Integrating both approaches should improve your results for calling individuals especially if yo ...
written 3.5 years ago by mdm-two200
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Answer: A: Variant Function Prediction
... Other potential candidates: Gemini: GEMINI: integrative exploration of genetic variation and genome annotations http://quinlanlab.org/pdf/Gemini-Quinlan-Stroke-UVA.pdf PLoS Comput Biol. 2013 Jul;9(7):e1003153. doi: 10.1371/journal.pcbi.1003153. Epub 2013 Jul 18. GERP ( integrated in Ensembl VEP? ...
written 3.5 years ago by mdm-two200
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Answer: A: Pindel Somatic Calls?
... The setup is described in the online user manual: http://gmt.genome.wustl.edu/pindel/current/user-manual.html There is a also a screencast from Kai Ye: https://www.youtube.com/watch?v=SQKHXfPSJfE&feature=player_embedded ...
written 3.5 years ago by mdm-two200
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Comment: C: How To Get The Size Of Sv With Respect To Breakdancer Output
... Tigra was published and Ken Chen's group is actively developing it. See: http://bioinformatics.mdanderson.org/main/TIGRA For small deletions and insertions you should consider Pindel as well. The position of the deletion can't be exactly determined using the BreakDancer method... that's why yo ...
written 3.5 years ago by mdm-two200
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Comment: C: How To Get The Size Of Sv With Respect To Breakdancer Output
... The predicted size is of the deletion of 1842. Because BreakDancer only examines read pairs spanning event, the coordinates are the outermost boundaries of the variant. (The span should always be larger than the size of any deletion and can be smaller than the size of an insertion). If you want ...
written 3.5 years ago by mdm-two200
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Answer: A: Variant Effect Predictor On Domain Level
... Q(1) Is there any tool to take Ensembl variant effect predictor output to mark the synonymous and non synonymous mutations on the protein domain level? For protein level annotation you can can try using the --domains option of VEP http://useast.ensembl.org/info/docs/tools/vep/script/vep_options.htm ...
written 3.7 years ago by mdm-two200
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Comment: C: Are There Any Tools To Convert Gatk Vcf Format To A Maf File ?
... vcf2maf.py converts a VCF to TCGA Mutation Annotation File (MAF). The galaxy tool vcf_to_maf_customtrack1 (URL above) converts a VCF file into a Multiple Alignment Format (MAF) file suitable for display at genome browsers. ...
written 4.0 years ago by mdm-two200
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Answer: A: Vcf To Maf (Mutation Annotation Format) Conversion ?
... See www.biostars.org/p/74822/ and seqanswers.com/forums/showthread.php?t=16740 ...
written 4.0 years ago by mdm-two200
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Answer: A: Converting Vcf File To Maf
... Same question answered here: http://seqanswers.com/forums/showthread.php?t=16740 converting VCF file to MAF ...
written 4.0 years ago by mdm-two200
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Answer: A: How To 'Genome Music Play' Using Wig File Instead Of Bam File?
... I think you will need to use music bmr calc-wig-covg to generate the gene coverage files. ...
written 4.1 years ago by mdm-two200 • updated 4.1 years ago by Istvan Albert ♦♦ 73k

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