Questions tagged [picard]

for questions about Picard; popular open-source toolkit focused primarily on sequence and variant data manipulation.

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62 views

Marking optical or PCR duplicates with picard vs. samtools flagstat

I am trying to identify the best library prep method for noninvasive prenatal test samples, to be sequenced with Illumina Novaseq. One metric that I am evaluating is the number/ percentage of PCR or ...
4
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1answer
59 views

How does picard's MarkDuplicate handle unmapped reads?

Our BAM files are created according to a "lossless" alignment procedure [1] from the Broad Institute GATK documenation and involves re-adding the ...
2
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1answer
335 views

How to demultiplex a mix of single-indexed and dual-indexed samples

The problem If I have a sample sheet that contains both single-indexed and dual-indexed samples, I can split it up into two sample sheets and then run bcl2fastq on each one. However, when doing this, ...
3
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2answers
448 views

Is there a safe catch-all adapter sequence for trimming?

I would like to trim/mark adapters using trimmomatic or picard MarkIlluminaAdapters from a series of Illumina Paired-End read fastqs. The fastq files may have been done using different kits or ...
1
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1answer
36 views

Including Picard tool in galaxy

I am running the Picard tool CollectSequencingArtifactMetrics in galaxy (locally in my pc). The output files are saved into disk and not passed to stdout and (I guess) they can't be passed as output ...
0
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1answer
144 views

Picard validation error regarding bin field of BAM file

I am sure I set the path right but whatever I am trying the command not working Any help please? ...
1
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0answers
101 views

CollectHsMetrics base coverage output has overlapping targets

I am trying to get base coverage information, and am using the --PER_BASE_COVERAGE output from Picard tools to get a text file of base level coverage. However, some ...
3
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1answer
67 views

Determining Read Groups

Which Read Groups are correct: ...
5
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1answer
171 views

How to validate that BAMs have been downloaded correctly?

I currently have several hundred BAM files which were downloaded by someone else. These have remained untouched---before working with them, I would like to double-check that these BAMs have been fully ...
4
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2answers
568 views

GATK CombineVariants complains the contig order in the VCF files

I have called variants on two strains of C. elegans separately. I now want to merge the VCF files into one using the following code: Create a sequence dictionary of the reference sequence Sort the ...
1
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1answer
350 views

How can I subset a reference based on only the first chromosome?

I have the GATK FASTA reference for hg19. I would like to subset this based on the first chromosome. Normally what I do is open the FASTA as a text file, and then delete all other chromosomes except ...
2
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1answer
98 views

Picard CollectGcBiasMetrics ignoring certain chromosomes/sequences

What's the easiest way to run Picard GCBias ignoring certain chromosomes/sequences in the reference? Looking at the CollectGcBiasMetrics, it seems there isn't a bed file option that can be passed. <...
6
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1answer
906 views

How to remove all BAM read groups from all reads (not just the header)?

I have problem with one my BAMs---it appears to have invalid read groups. Normally when I have such a problem, I remove all the read groups from the BAM header as follows: ...
6
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1answer
432 views

low-memory high-speed replacement for Picard MarkDuplicates

I am running Picard MarkDuplicates with the following parameters below. On the file described, it takes about 41.6Gb of RAM memory and about 20-25 minutes to compute (only uses 1 core AFAICS). ...