Luis Paulin
Luis Paulin
Yes, however we have received some reports that sometimes variants are missing, if that is the case for you please let us know
Dear tnguyengel, did you manage to run the 5000 samples? We just released a new version (2.3.3) that aids with some issues and are improving on merging large datasets. Your...
Hello Jake, thanks for pointing this out. Is it possible that you could share use one or two examples of SNP entries with that format so that we could catch...
Hello Jake, thanks for the detailed information, I will check it out and reach back asap. Luis
Hi Li, The message you see is a warning, not an error. This happens when as it is stated the index is older than the alignment. The warning is given...
Hi Li can you please upload the full output log from Sniffles, if possible attached to the message Best Luis
Hello Sumudu It looks like Sniffles is only using the reads marked in red for that call. Can you confirm it with the read names you have in the INFO...
Dear Sumudu, here are some insights: 1. the `PASS` variant (left to the 12.5kb ones) is clearly shown in the blue haplotype 2. the 12.5kb DEL has a GT filter...
Dear @annerilotter There are a couple of values in the INFO filed that may help you as well: `STDEV_POS` Describes the standard deviation of structural variation start position and `STDEV_LEN`...
Hi @SergeWielhouwer, could you please share with us the header of the SNV-VCF file please. You can use the following command: ```bash bcftools view --header-only file.vcf.gz > file_vcf_header.txt ``` We...