ShannonDaddy

how to set umi mismatch and umi cluster method?

2

Hi, when i using gencore, can I set umi mismatch or the clustering method like 'directional adjacency' in umi-tools?

how to see the version of genefuse?

1

Hi, I got the genefuse by git clone on the command line, and make, finally, I got the binary genefuse, but I can't find the version of it. How to...

low complexity trimming or masking for nanopore reads

3

Hi, is there any option for fastp to trim or masking low complexity region in nanopore reads? As I always see some low complexity reads as follows: @147b5220-2abe-4d1f-9507-b7d278e33efa ATGTGCTTCAGTTCAGTTACGTGTGCTGGTGCTGTCACTACTCAACAGGTGGCATGAATTAACTTACTTGCCTGTCGCTCTATCTTCGGCGTCTTGGGTGTTTAACCTACACTACACACACACCACACCACACACACACACACATACACACACCCCACAGCACACGCCCCCCACACACACAGACACCACACACACACCGCACACCACACTACACACACACCACACACCACACCACACACTACACACACACCACACACCACACCACACACACACCATACACACCACACCACACACCACACCACACACACCACACACACACAAACACACACACACACGCACACCGCCACCTGCACACACTACACACACACCACACACCACACCACACACCCACACACACACCACACACACCACACACACCACACCATACACACACACCACACACACACCACACACTACACACACCACACACACACCACACACACACCACACACAGCACACACCACATCCCACACACACACACCACACACCACACCACACACTACACACACACCACACATCGCACACCACACCACACACACCACACACCACACACACACTGCACACCACACACACCGCACACCACACACTACACACACACCACACACCACACACACCACACACACACCATACACCACACACGCACCACACACACACACCACACACCACACGCACACCACACACACCACACACACACCCATACCACACCACACACACCACACACACCACACACCACACACAGGTTAAACACCCAAACGGACATACCGCAATATCAGCACCAACAGAAGGTTAATTCATGCCACCCATATTTGGTCTTTACGTTGTTATGTGCTTCGTTCAGTTACGTATTGCTGGTGCTGCAGAGCTTTGACTAAGGAGCATGTTAACCTTTCTGTTGGTGCTGATATTGCGGCGTCTGCTTGGGTGTTTAACCTCATGAAAACGCAAATATTTTAAAAATGTAGCTTTATGCAAAAGCAAGCTGAAAGGTTTCTTGTTGCATTGTTGTACGTTGAAGCTCAGTCACTTTGCTGACATTGAGTTTCTTTTTCTCCCAGTCACCCTTCTCCACCAATGCTACTATTTATGCGAAGTGTCGGAAATTAACTTCTCATGTGACCACCCAATTCGGTTCCAGTCGCTTGGAAATGTAATCTATTC @d4fc11d4-ef02-42b2-a908-2adc747e10b5...

can strelka2 export variants in halplotype form?

2

Hi, strelka team I was really impressed by the model and performance of strelka in calling somatic mutations. But I have a question on the variant form in the vcf...

support synonym or equivalent name when calling taxid_from_name

4

Hi, when I call function taxid_from_name to get taxid, I get some warnings. my code: import taxopy ncbi_taxdb_dir = "database/ncbi_taxonomy" taxdb = taxopy.TaxDb(nodes_dmp=f"{ncbi_taxdb_dir}/nodes.dmp", names_dmp=f"{ncbi_taxdb_dir}/names.dmp", merged_dmp=f"{ncbi_taxdb_dir}/merged.dmp", keep_files=True) taxid_list = taxopy.taxid_from_name('Lactobacillus fermentum',...

What's the difference between --collapse and --crushvcf options of Pisces

2

Hi, I can't tell the difference of --collapse and --crushvcf options of Pisces from the documents and command-line help, please help me out. Thanks a lot!

Gemini 5.3.0.0 Nullable object Error

1

Hi I got the Nullable object Error when I was using Gemini in Pisces 5.3.0.0, and I can't figure out why, please help me. I have also post the issue...

clustered snps can't be merged by scylla

2

Hi, I found that some clustered snps can't be merged by scylla. I don't see why. Attached is my igv snapshot, bam files and scylla options.  [ScyllaLogs.zip](https://github.com/Illumina/Pisces/files/4854716/ScyllaLogs.zip) [igv_snpshot.zip](https://github.com/Illumina/Pisces/files/4854730/igv_snpshot.zip) [bam_files.zip](https://github.com/Illumina/Pisces/files/4854943/bam_files.zip)...

Hi, how to deal with multiple variants in a small region

5

Hi, how to deal with multiple variants in a small region, is there a way to combine them to one variant by Pisces or other tools? Attached file describes the...

option to filter clustered snps

2

Hi, is there an option for Pisces to filter clustered snps, usually they are false postives.