33 results in 0.0032 seconds.
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No mutations in BAM (IGV) but a mutation in final VCF?
I use GATK 4.0 for the variant calling pipeline. my steps involve MarkDuplicates, BaseRecalibration, ApplyBaseRecalibration and HaplotypeCaller. When... -
Counting Reads in BAM file per genomic position
Hello,
I am looking for a tool or script that counts the number of reads in a bam file by position, and takes into account only successfully...Last edited by C9r1y; 11-24-2015, 02:31 PM. -
SNP coverage using Pile up From RSamtools
Hi, I am using pile up from R Package, ‘Rsamtools’. I could not get the correct coverage for the SNP positions I am looking for in my BAM files. The...Last edited by MAPK; 11-05-2015, 11:45 PM. -
Calculating coverage of SNPs
Hello all,
I'm having a problem calculating the depth of coverage of a set of known variants (SNPs). What I want to know is 1) what percentage...Last edited by aprilw; 08-28-2015, 04:31 AM. -
Counting the total number of SNPs in a transcript
Hi,
I have RNAseq data that has been aligned to reference transcriptome and the aligned bam file is sorted and indexed.
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Lack of paired mate in BAM file
Hello,
When I use BWA and samtools to align sequences to a reference host genome and extract the non-host DNA I get the following warning... -
IGV colors entire BAM file as inversions
I'm using the Integrative Genomics Viewer (IGV) to view the alignments achieved from TopHat.
I have four samples (and thus four BAM files).... -
Cufflinks: sort order of reads in bams must be the same
Hi all,
I am trying to run cufflinks on STAR-aligned reads. After converting to BAM and executing "sort" command I do this:... -
HTseq-count error: mate pairs cannot be matched
Hi guys, I'm having some trouble running HTseq-count on paired end RNA-seq data. I use the following command to run HTse-count:
...Code:htseq-count
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How to convert CRAM back to BAM using samtools
Hello everyone,
I just installed samtools v1.0 and want to test CRAM feature. I converted .BAM file to .CRAM and It was successful. Now... -
Specifying read group info for multiple samples per lane in SAM/BAM files (for GATK)
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Samtools 0.1.19, Unbuntu 14.04, problem getting a consensus
Hello all,
I'm having trouble using samtools to get a consensus of a small viral genome and I'm fairly certian its user error. I am very... -
Exon locations in Novel Transcripts
Hi,
I found several novel transcripts using RNA-Seq data (paired-end reads), in intergenic regions. Some of them have 2 or 3 exons.
Now... -
Estimated very low inset size from bam file using picard
Hi,
I have used picard's CollectInsertSizeMetrics program to collect insert size matrices from bam file. Although program worked quite... -
Online tools to generate count tables from sam/bam files
Does Galaxy or any other online tools offer methods to generate a count table from bam or sam files?
