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Hi Platinum Devs,
I am interested in running the HMFtools pipeline on GCP, but I already have my files aligned with bwa-mem. Is there support for starting with aligned BAMs using Platinum/could you…
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Hi Alex,
I got a problem while generating BAM files using STAR 2.7.9a. The error message was following:
`EXITING because of FATAL ERROR: number of bytes expected from the BAM bin does not agree w…
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samtools view -F 1294 includes flag 2048 （supplementary alignment），but samblaster --discordantFile did not include flag 2048 （supplementary alignment），as well as speedseq， which used samblaster --disc…
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Hi Alex,
I am using STAR2.7.6a and use STARsolo to deal with a 10x dataset.
I wonder how I can get deduplicated bam file as the output (Aligned.sortedByCoord.out.bam).
Now, I can see reads with ex…
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Hi there
Any idea to solve the following issue ?
....
[I::dump_links_from_bam_file] 658 million records processed, 213396899 read pairs
[I::dump_links_from_bam_file] 659 million records proc…
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Hi! Is it possible to include the --bam-list option from freebayes to read in a list of BAM files to be analyzed rather than specifying each individual BAM file?
Thanks
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Can I use BAM files where RNA-Seq reads have been mapped to the genome rather than the transcriptome?
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@mukarramtahir
Was looking through the BAM reader section of your code. I saw that your using samtools view to load in all of the lines of the code at ounce:
![image](https://cloud.githubusercontent…
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LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
Distribu…
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Hello,
I am getting an error when trying to run the software. Here is my code:
```
seGMM --vcf my.vcf \
--input bam.file --alignment_format BAM \
--reference_additio…