Questions tagged [picard]
for questions about Picard; popular open-source toolkit focused primarily on sequence and variant data manipulation.
18
questions
3
votes
0
answers
15
views
Picard's CollectGcBiasMetrics gc-bias plot- help with interpretation
Setup
I ran picard's CollectGcBiasMetrics tool for my WES sample, with the intention of assessing the performance of the Exome capture panel in terms of the uniformity of read coverage at various %GC ...
- 171
3
votes
1
answer
162
views
Singularity & Picard
I am trying to run Picard in Singularity and try as I might I cannot seem to find the path to use. For example with GATK 4.4.0.0 I use the following path:
...
- 189
1
vote
1
answer
134
views
Estimate insert size for single-end data with picard CollectInsertSizeMetrics
I have a BAM file generated from single-end data and I want to estimate the insert size using picard's CollectInsertSizeMetrics as follows:
...
- 323
-4
votes
1
answer
188
views
Getting error in running GATK
I am trying to making a fasta doc using GATK tools but I don't know what does this error say
Server2:/data2/RNASeq/Angel/gatk$ ./gatk CreateSequenceDictionary -R reference.fa
Using GATK jar /data2/...
- 1,791
2
votes
2
answers
1k
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 ...
- 273
4
votes
1
answer
233
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 ...
- 319
3
votes
2
answers
2k
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, ...
- 131
3
votes
2
answers
1k
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 ...
- 319
1
vote
1
answer
53
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 ...
- 585
0
votes
1
answer
446
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?
...
- 1,791
1
vote
0
answers
166
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 ...
- 31
3
votes
1
answer
190
views
6
votes
1
answer
298
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 ...
- 1,373
4
votes
2
answers
819
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 ...
- 2,449
1
vote
1
answer
2k
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 ...
- 1,373
2
votes
1
answer
154
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.
<...
- 2,274
7
votes
1
answer
2k
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:
...
- 1,373
7
votes
1
answer
701
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).
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- 2,274