9
votes
Accepted
How to validate that BAMs have been downloaded correctly?
samtools quickcheck is all you need. From the manual:
Quickly check that input files appear to be intact. Checks that beginning of the file contains a valid header ...
- 19.6k
7
votes
Accepted
How to remove all BAM read groups from all reads (not just the header)?
You might have to manually strip those auxiliary tags off:
...
- 19.6k
5
votes
Accepted
Marking optical or PCR duplicates with picard vs. samtools flagstat
There are duplicates, in this line:
1636809 + 0 duplicates, gives 1636809/26595942 = 0.06154356
According to samtools documentation for flagstat:
Provides counts for each of 13 categories based ...
- 1,678
5
votes
Accepted
Estimate insert size for single-end data with picard CollectInsertSizeMetrics
CollectInsertSizeMetrics does not estimate but (as by the name) collects insert size metrics, which is nothing different than parsing the TLEN field from the BAM ...
- 1,108
4
votes
Determining Read Groups
Usually it doesn't actually matter, but if you want it to be very correct:
...
- 19.6k
3
votes
GATK CombineVariants complains the contig order in the VCF files
Answered in the GATK forum
Try regenerating the index files for your VCFs. Picard SortVcf doesn't do it for you iirc, so when GATK looks at the index files (before opening the VCFs themselves) it ...
3
votes
Accepted
How can I subset a reference based on only the first chromosome?
It sounds like you want samtools faidx foo.fa followed by samtools faidx foo.fa chr1 > your_subset_file.fa (or whatever the ...
- 19.6k
2
votes
low-memory high-speed replacement for Picard MarkDuplicates
As you suggested, sambamba is faster at marking duplicates than picard (it's also multithreaded). Recent versions of samtools have a rewritten duplicate marking algorithm, though I doubt it'll be as ...
- 19.6k
2
votes
Accepted
GATK CombineVariants complains the contig order in the VCF files
GATK cannot combine VCF files generated by Sniffles, the variant caller that I used to call structural variants (answer from the GATK team).
- 2,459
2
votes
Is there a safe catch-all adapter sequence for trimming?
Alternatively, I really like using bbduk which is part of the BBMap suite.
I've processed every nascent sequencing dataset that has been published, and found a lot of quirky errors with older ...
- 141
2
votes
Is there a safe catch-all adapter sequence for trimming?
You're best off just using fastp or Trim Galore!, both of which will determine the adapter sequence for you. Trim Galore! uses a ...
- 19.6k
2
votes
Accepted
Singularity & Picard
Assuming you've pulled the latest broadinstitute/picard container, your first attempt should have produced the expected result:
...
- 3,059
2
votes
Marking optical or PCR duplicates with picard vs. samtools flagstat
@StupidWolf's answer is correct -- that first number in the flagstat output is what you want to look at to see the number of reads marked as duplicates. I wanted to add that the number given in the ...
2
votes
How does picard's MarkDuplicate handle unmapped reads?
From the Picard documentation:
DUPLICATION METRICS:
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.
UNMAPPED_READS The total number of unmapped ...
- 1,374
1
vote
How to demultiplex a mix of single-indexed and dual-indexed samples
I'm late to the party but simply run cellranger mkfastq twice, with different arguments for the mask and with --filter-dual-index...
- 111
1
vote
Including Picard tool in galaxy
Picard, like most tools, prints logs to stderr.
It should be in the Galaxy history. Are you using a version of picard from the toolshed (if so, which one)? You might set ...
- 19.6k
1
vote
Accepted
Picard CollectGcBiasMetrics ignoring certain chromosomes/sequences
The proper solution is to use a different tool (some of this you could do with computeGCBias in deepTools). But since you don't want to do that, you'll have to ...
- 19.6k
Only top scored, non community-wiki answers of a minimum length are eligible