Deletions, Translocations And Cnv From Rna-Seq
Is it possible to find out deletions tarnslocations and / or copy number variations between RNA-seq data of control vs treated samples. The data is PE with enough coverage ( say around 30X).Thanks
View ArticleHow To Make A Circular Plot Of Snps And Indels ??
Hello everybody,I am analysing SNPs and INDELs in several prokaryotic genomes of the same strain. My goal is to compare them with a reference genome . I would like to learn how to plot the SNPs in a...
View ArticleHow to call low frequency snp/indel with GATK's HC/UG
i want to call snp/indel with low frequency, like DP=100, ALT=10.how to set HC/UG ?with UG, i run with :--min_indel_count_for_genotyping 2--min_indel_fraction_per_sample 0.05get a nice result, but i...
View ArticleGatk Threshold Parameter For Clipping Of Reads During Indel Calling Running...
GATK 1.6 claims to apply a Q20 threshold to clip ends of the reads for the indel caller:http://www.broadinstitute.org/gatk/guide/article?id=12373. Indel Calling with the Unified Genotyper [...] while...
View ArticleNext Gen Sequencing Indel Realignment With The Genome Analysis Toolkit (Gatk)
As I continue to add steps to my SNP/Indel discovery workflow, the latest recommendation is local realignment around Indels using GATK following the initial alignment step. I have just commenced the...
View ArticleIndel Notation In Variant Calling
HelloI am sorry for the basic question but I am struggling to find any details of the nomenclature of indels by variant calling software. Unfortunately i am unable to access the details of the software...
View ArticleHow To Call Variants (Snp, Indel, Sv) On A Bac Contig Aligned With Bwa Mem To...
I aligned a BAC contig (assembled from sanger sequences) to a reference genome using BWA-mem. The output alignments are very similar to the best end to end alignment I got from aligning the bac contig...
View ArticleMerge indel VCF files
I am merging tons of indel VCF files using vcf-merge. It does not work and I found these VCF files cannot pass the vcf-validation. Is there any way to merge indel VCF files? Thanks! #CHROM POS ID REF...
View ArticleHow Best To Add Custom Variation Track To Ucsc Browser?
I have generated sequence variants (SNPs/INDELs) by NGS resequencing and would like to display them on the UCSC browser (I have resequenced against a UCSC reference genome). Obviously i could use BED...
View ArticlePindel Error: Shiftedvector Out-Of-Range Error
Hello,I’ve been running pindel like so: pindel --config-file bam_config.txt --fasta /path/to/hg19/fasta/ --chromosome ALL --output-prefix /path/to/outputand I’ve noticed a lot of my pindel jobs fail...
View ArticleGatk Indel Realignment Error - Mismatch In Index Files And Dict File
Greetings,I am aligning pooled sequencing data to a new renferece genome. GATK won't generate intervals because not every scaffold in the reference is found in my bam index?What am I missing? It seems...
View ArticleHow To Retrieve Reads Supporting A Snp/Indel
I used samtools and varscan for variant calling like this:samtools mpileup \ -f genome.fa \ tku.sorted.rmdup.bam \ | java -jar VarScan.v2.3.5.jar pileup2snp \ --min-coverage 8 \ --min-reads2 2 \...
View ArticleStrange variant call it show a indel but looks like a SNP
Hello all, i have a variant from a ION PGM sequencing, called with the ION Torrent variant caller plugin CHR POS ID REF ALT chr22 44324726 . T TG The flow cell...
View ArticleProgramming Challange: Pairwise Alignments To Multiple Alignment
I have a set of 10-12 very closely related chromosome sequences (from different strains) aligned to a "single" reference chromosome. Now I need to generate multiple sequence alignment of these without...
View ArticleNgs Tool Analysis For Snp&Indel Calling Of Pooling Data
What are the best and most used analysis tool actually, for SNP and indel calling of pooled data?I'm using: GATK Freebayes that have specified options for data in pool.Now I have found CRISP.Are there...
View ArticleSamtools Indels -- Filtering Only Hits With Insertion In The Reference In The...
Can anyone suggest how to use samtools to filter only hits where there is a insertion in the reference that splits the sequence hit roughly by the middle? My sequences are in the range of 100-1000bp...
View ArticleSamtools: Local Realignment Around Indel
In samtools mpileup, adjust the option -m and -F to control when want to initiate indel realignment, any guideline to set the values for m and F for high coverage data (eg. >=20X)low coverage data...
View ArticleGatk Threshold Parameter For Clipping Of Reads During Indel Calling Running...
GATK 1.6 claims to apply a Q20 threshold to clip ends of the reads for the indel caller:http://www.broadinstitute.org/gatk/guide/article?id=12373. Indel Calling with the Unified Genotyper [...] while...
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Indel Left/Right Alignment
When matching indels between different VCF files (generated by different callers), there is this issue with left / right indel alignment, For example: Here is a real example for one indel (from the...
View ArticleBenchmarking Read Alignment And Variant-Calling Algorithms (For Dummies)
Hi all, I am wondering if there is a good step by step guide of how to benchmark alignment and variant calling software. I do understand the premise e.g.Generate reads with known mutations Align to...
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