yxt

iostream error 4

2

Tried to run dragmap, the commands are: ` dragen-os -r /paedyl01/disk1/yangyxt/indexed_genome/hg19 -1 /paedyl01/disk1/yangyxt/wgs/40_samples_help/download_data/clean/TCA-082A/forward_read/TCA-082A-542_1.fastq.gz -2 /paedyl01/disk1/yangyxt/wgs/40_samples_help/download_data/clean/TCA-082A/reverse_read/TCA-082A-542_2.fastq.gz --num-threads 10 --Aligner.sec-aligns 5 --fastq-offset 30 --Aligner.sw-method dragen --verbose --RGID TCA-082A --RGSM TCA-082A --output-directory /paedyl01/disk1/yangyxt/wgs/40_samples_help/download_data/clean/TCA-082A...

Pls help provide these default resources... The determination of the gene list for BP2 and PP2 is already part of the interpretation workload. Thanks!

locale setting failed with latest docker image.

4

**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.4/docs/FAQ.md**: **Describe the issue:** According to the running log: the setlocale failed when trying to change LC_ALL to 'en_US.UTF-8' **Setup** - Operating system: CentOS7 -...

DataLoss Error with Tensorflow

7

**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.4/docs/FAQ.md**: Yes **Describe the issue:** At the call_variants.py step, running into error that tensorflow.python.framework.errors_impl.DataLossError: truncated record at 19179998357' failed with EOF reached (A clear and...

bcftools query cannot accurately match the INFO tag sharing a common prefix with other INFO tags

1

I tried to run `bcftools query -f '%AC-controls_and_biobanks\n' ` but failed to get the field "AC-controls_and_biobanks", Instead I get value from INFO field "AC" concatenated with "-controls_and_biobanks" How can I...

Can CrossMap lift bam tag values as well? Like NM tag, MD tag

3

The same as the title.

No GT field in merged vcf file

1

I just tried to merge vcf files separately from gridss, delly and pindel and found that no GT field is in the merged vcf file. The command I ran is:...

papaemmelab / mergeSVvcf: invalid chromosome issue with pysam

12

I have test the run with a simple vcf file from DELLY, (test convert all symbolic records to BND records) and it failed. The specific error log is : ```...

swifter.groupby() does not support with dropna=False

5

I found that the swifter groupby apply chain will encounter the error when trying to sort index, if I set dropna to False for the groupby step. Here is the...

**Only bug reports!** The D version of Sambamba is in maintenance mode. Use the github issue tracker to report bugs *only*. For comments, questions and features, please use the google...