User: ttmigueltt

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ttmigueltt10
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Posts by ttmigueltt

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Longitudinal QC Platforms for NGS Data
... I'm looking for platforms, both commercial and open source, that deal with tracking QC data over time, over many samples, and looking for trends, alerting the user to poor/failing samples. Currently the tools I have identified that do this (to some extent) are: * Commercial: * [Euformatics Omno ...
qc sequencing written 5 weeks ago by ttmigueltt10
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Extracting the full read ID when converting from BAM -> FASTQ
... I want to ensure I can convert my BAMs back to FASTQ without any loss of data. However, I have noticed that, when running `samtools fastq`, the reads that come out look different from the reads I originally aligned. In particular, they seem to have lost the second segment of the read ID that contain ...
fastq bam samtools bwa written 6 months ago by ttmigueltt10 • updated 6 months ago by toralmanvar760
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Comment: C: Stop GATK MergeBamAlignment from unmapping reads
... I think it's for two main purposes: - When you are using the BAM format to store metadata about your unmapped reads, you sometimes have to convert your unmapped BAM back to fastq format in order to actually align the reads. For example, BWA doesn't yet accept an unmapped BAM as input. Thus, using t ...
written 6 months ago by ttmigueltt10
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Stop GATK MergeBamAlignment from unmapping reads
... I'm using GATK 4.0.11.0-0's [MergeBamAlignment](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/picard_sam_MergeBamAlignment.php), which is supposed to be able to combine an aligned BAM and an unaligned/unmapped BAM without losing any data or adding any duplicates. I've been ...
gatk4 gatk alignment bam mergebamalignment written 6 months ago by ttmigueltt10 • updated 6 months ago by finswimmer11k
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Comment: C: Two inputs combining to a single command line argument in CWL
... Is this not using JavaScript here? If not, is there documentation on this string interpolation? ...
written 12 months ago by ttmigueltt10
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Comment: A: Two inputs combining to a single command line argument in CWL
... . ...
written 12 months ago by ttmigueltt10
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Two inputs combining to a single command line argument in CWL
... The invocation of [VarDictJava][1] in paired variant calling mode is VarDict -b "/path/to/tumor.bam|/path/to/normal.bam" Now obviously in my CWL I would like the tumour and normal BAM to be separate inputs. However, I'm not sure how to combine these into a single command line argument in the ...
cwl written 12 months ago by ttmigueltt10

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