Applications Of Indexed Bam Files

applications of indexed bam files

Using VarScan 2 for Germline Variant Calling and Somatic

This tool samples indexed BAM files and plots a profile of cumulative read coverages for each. All reads overlapping a window (bin) of the specified length are

applications of indexed bam files

BamTools HCC-DOCS - HCC Documents

EvE Free (this app) Price: Requires the BAM files to be indexed. The website and all software applications

applications of indexed bam files

samtools Tutorial Quinlan Lab @ UU

... a comma-separated list of BAM/CRAM files generated by BWA-MEM and sorted and indexed applications. HipSTR HipSTR can analyze both BAM and CRAM files

applications of indexed bam files

HipSTR Genotype and phase short tandem repeats using

samtools “index” Indexing a genome sorted BAM file allows one to quickly extract alignments overlapping particular genomic regions. samtools index sample

Applications of indexed bam files
applications of indexed bam files

Converting samtools BAM to consensus FASTA sequence?

Indexing: IGV requires that both SAM and BAM files be sorted by position and indexed, and that the index files follow a specific naming convention. Specifically, a BAM index file should be named by appending .BAI to the bam file name. A SAM index filename is created by appending .SAI.

applications of indexed bam files

Conversion of mapreads output to GFF SAM or BAM format

Overview of the splitChromosome function of bamUtil. The splitChromosome option on the bamUtil executable splits an indexed BAM file into multiple files based on the

applications of indexed bam files

Using VarScan 2 for Germline Variant Calling and Somatic

Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers.

applications of indexed bam files

BamTools HCC-DOCS - HCC Documents

Read Only One Reference/Chromosome from Sorted/Indexed BAM Files. This example reads in the inputFilename bam file and writes it back out section by section to the

applications of indexed bam files

Oracle Business Activity Monitoring

Converting samtools BAM to consensus FASTA sequence? I have a .bam file and I used it to extrapolate consensus FASTA sequence. samtools index $bam.bam.

applications of indexed bam files

BAMQL a query language for extracting reads from BAM files

This is highly beneficial for a number of applications discussed in Position-sorted BAM files can be indexed so that all reads aligning to a locus can be

applications of indexed bam files

Introduction to RNA-seq Analysis Purdue University

Dave's Wiki. Dave's Wiki Loading... #index the bam file first samtools index test.bam samtools view test.bam chr1:200000-500000 #all reads mapping on

applications of indexed bam files

I-ATAC interactive pipeline for the management and pre

We have created a query language that gathers reads using or integration into applications. The query language provides a indexed BAM is provided, the query

applications of indexed bam files

Sam Library Usage Examples Genome Analysis Wiki

10x Genomics Chromium Single Cell Gene Expression. Cell Ranger 2.2 (latest), printed on 10/01/2018. Barcoded BAM. The cellranger pipeline outputs an indexed BAM file

Applications of indexed bam files - Integrative Genomics Viewer (IGV) tutorial

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