Hywel Williams
@genefiddler.bsky.social
Senior Lecturer in Bioinformatics @cardiffuni
I am fascinated about how genomic variation leads to disease & how we can use this knowledge to improve treatment.
I am fascinated about how genomic variation leads to disease & how we can use this knowledge to improve treatment.
Finally, we show that there is a significant enrichment (9.5x10-9) of these pathogenic variants in patients with neurodevelopmental disorders.
The reasons for this are unclear but suggests for such patients this would be a good first approach.
Pls read and RT. If you have questions DM me.
4/4
The reasons for this are unclear but suggests for such patients this would be a good first approach.
Pls read and RT. If you have questions DM me.
4/4
May 27, 2025 at 3:10 PM
Finally, we show that there is a significant enrichment (9.5x10-9) of these pathogenic variants in patients with neurodevelopmental disorders.
The reasons for this are unclear but suggests for such patients this would be a good first approach.
Pls read and RT. If you have questions DM me.
4/4
The reasons for this are unclear but suggests for such patients this would be a good first approach.
Pls read and RT. If you have questions DM me.
4/4
It's important because pre-filtering genomic data to identify these variants is a rapid way to diagnose patients, leaving more time to analyse additional patients.
If you don't have trio data don't worry, we show that 81% of variants in high CCRs are also pathogenic.
3/4
If you don't have trio data don't worry, we show that 81% of variants in high CCRs are also pathogenic.
3/4
May 27, 2025 at 3:10 PM
It's important because pre-filtering genomic data to identify these variants is a rapid way to diagnose patients, leaving more time to analyse additional patients.
If you don't have trio data don't worry, we show that 81% of variants in high CCRs are also pathogenic.
3/4
If you don't have trio data don't worry, we show that 81% of variants in high CCRs are also pathogenic.
3/4
Headline metric:
We show that >91% of de novo variants in highly Constrained Coding Regions (CCR) are clinically diagnosed in #raredisease patients as pathogenic.
This corresponds to around 9% of the cohort.
Question: Why is that important?
2/4
We show that >91% of de novo variants in highly Constrained Coding Regions (CCR) are clinically diagnosed in #raredisease patients as pathogenic.
This corresponds to around 9% of the cohort.
Question: Why is that important?
2/4
May 27, 2025 at 3:10 PM
Headline metric:
We show that >91% of de novo variants in highly Constrained Coding Regions (CCR) are clinically diagnosed in #raredisease patients as pathogenic.
This corresponds to around 9% of the cohort.
Question: Why is that important?
2/4
We show that >91% of de novo variants in highly Constrained Coding Regions (CCR) are clinically diagnosed in #raredisease patients as pathogenic.
This corresponds to around 9% of the cohort.
Question: Why is that important?
2/4
I've written a more detailed description of my problem and some examples of the files/scripts I've been using on SEQanswers: www.seqanswers.com/forum/genera...
Remove unwanted contigs and update bam header -
SEQanswers
Hi,
I have some human genome data in bam format that I want to upload to some software (Congenica) to perform variant filtering.
The problem I have is that presently the data has been mapped to a refe...
www.seqanswers.com
March 6, 2025 at 1:12 PM
I've written a more detailed description of my problem and some examples of the files/scripts I've been using on SEQanswers: www.seqanswers.com/forum/genera...
It's patient data so unfortunately can't share the file, it's also very big. However, the header looks like this 👇and I need to remove the alt contigs, there's 1000s of them. That bit seems to work using samtools, it's then updating the head I'm struggling with.
March 5, 2025 at 6:51 PM
It's patient data so unfortunately can't share the file, it's also very big. However, the header looks like this 👇and I need to remove the alt contigs, there's 1000s of them. That bit seems to work using samtools, it's then updating the head I'm struggling with.
I seem to be able to remove the reads for the alt contigs but when I re-head the bam it all goes to 💩 and I go from >1B reads to ~600! Strangely the bam file is almost the same size so it seems to be a problem with the header?
If you have any ideas pls share and RT 🙏
2/2
If you have any ideas pls share and RT 🙏
2/2
March 5, 2025 at 5:24 PM
I seem to be able to remove the reads for the alt contigs but when I re-head the bam it all goes to 💩 and I go from >1B reads to ~600! Strangely the bam file is almost the same size so it seems to be a problem with the header?
If you have any ideas pls share and RT 🙏
2/2
If you have any ideas pls share and RT 🙏
2/2
pdf corrupted, can you please send a new link?
December 19, 2024 at 10:43 AM
pdf corrupted, can you please send a new link?
Great news Kim, keep up the good work!
December 9, 2024 at 12:32 PM
Great news Kim, keep up the good work!