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**1. What were you trying to do?**
Map short reads on a graph with vg map --surject-to bam
**2. What did you want to happen?**
I'd like to add the sample & read group IDs in the BAM output
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If you are using the "get_query_sequences" function from the "pileupcolumn" class, you cannot display the output in the Samtools mpileup format if you select all boolean options to be true.
I thin…
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Hi,
I have CRAM file of about 35G and I tried to convert it back to BAM. I used 32 cores machine, but it seems that only 1 core is doing a job. After ~20-30 mins there is no CPU activity and it was li…
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I am working with a non-model organism whose genome was constructed at the scaffold level. How can I automatically name all scaffolds from my bam file using the command --chrom? Thank you!
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Hi,
I recently ran into a very rare bug where I added U1,U2,U3,U4,U5,U6 and other snoRNAs to the genome and then defaulted the parameters to build the index. Then map my data on it. Then the program …
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Duplication is desired? This may be confusing for end users. Both samtools and picard are nearly always installed in locals as the first go-to tool packages.
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Thanks for this very useful workflow. To reduce runtimes, can I suggest adding a 'whitelist' rule to preprocessing? This could reduce runtimes considerably in situations where the targets are limited …
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On the develop branch 1b51e2d3e6ece2e5adf1ac7274246ee57fa9a81a
Consider example.bed file with 1 entry and 1 line:
```
chr1 1 5
```
Not that there is no empty line at the end
```julia
regions …
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Hi,
I am getting this error:
2018-07-06T10:48:27.499694345Z [2018-07-06T10:48:27.499530Z] [4beb0927f133] [14_1] [WorkflowRunner] [ERROR] [2018-07-06T10:48:10.850255Z] [4beb0927f133] [14_1] [getCh…
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Hi Dr.zhang
Thanks your great work in ALLHIC !
I got an error when I run `filterBAM_forHiC.pl sample.bwa_aln.REduced.paired_only.bam sample.clean.sam`. There is no header information in `sample.clea…