User: ttmigueltt

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ttmigueltt0
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Posts by ttmigueltt

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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 5 days ago by ttmigueltt0 • updated 5 days ago by toralmanvar720
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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 8 days ago by ttmigueltt0
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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 9 days ago by ttmigueltt0 • updated 9 days ago by finswimmer8.0k
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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 6 months ago by ttmigueltt0
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Comment: A: Two inputs combining to a single command line argument in CWL
... . ...
written 6 months ago by ttmigueltt0
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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 6 months ago by ttmigueltt0

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