User: Parth Patel

gravatar for Parth Patel
Parth Patel40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
3 years, 11 months ago
Joined:
4 years, 7 months ago
Email:
p***********@gmail.com

Posts by Parth Patel

<prev • 7 results • page 1 of 1 • next >
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Best way to enter Genomic Medicine? Curious and seeking exposure.
... I am very excited by the vision and problems found in genomic medicine. It allows me to do meaningful, impactful work while working on challenging software engineering-style problems. I am very strongly considering applying to a masters / phD program in genomics/ bioinformatics in the near future. H ...
exposure personalized forum medicine written 4.0 years ago by Parth Patel40 • updated 4.0 years ago by cyril-cros890
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Splice Site Frequency/ Pathogenicity Data
... Hello,  I need a data set that includes the frequency and pathogenicity labels for splice site mutations. I have tried to select these features from dbSNP, ClinVar, ESP, and PhenCode data sets I queried via EnsemblBioMart, but none of them actually contain frequency / pathogenicity labels. Any idea ...
ensembl biomart nnsplice pathogenicity splice written 4.6 years ago by Parth Patel40 • updated 4.6 years ago by Emily_Ensembl19k
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Comment: C: How to sort a VCF file lexicographically by chromosome number?
... That was really helpful -- a formatting issue was in fact giving me a corrupt VCF file. Thanks! ...
written 4.6 years ago by Parth Patel40
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Comment: C: How to sort a VCF file lexicographically by chromosome number?
... Hi Pierre, Thanks for the quick response. I tried your grep method and it yielded the same results as vcf-sort. The variants are sorted lexicographically by id, but the chromosome, position, and ref information is gone: ##fileformat=VCFv4.1 #CHROM POS ID REF ALT QUAL ...
written 4.6 years ago by Parth Patel40 • updated 8 months ago by RamRS24k
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How to sort a VCF file lexicographically by chromosome number?
...  Hello,       I have a large 155mb vcf file that I am trying to sort lexicographically by chromosome number (in the order 1,10, 11, 12 .. etc ) and then by position. I am trying to use vcf-sort from the vcf-tools perl package.    I have been running the command : perl vcf-sort myfile.vcf > o ...
vcf format lexicographic chromosome written 4.6 years ago by Parth Patel40 • updated 23 months ago by ATpoint24k
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Answer: A: Help obtaining splice site data from dbSNP!
... Thanks Michael and Emily!  This has made this process so much easier. I still need the genomic reference nucleotide for each variant. I understand that to gain a true reference, I would need to specify populations and look into allele frequencies. Would using the "ancestral allele" serve as a good s ...
written 4.6 years ago by Parth Patel40
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Help obtaining splice site data from dbSNP!
... Hi all,     I have been trying to download the splice site mutations found in dbSNP along with their corresponding genomic coordinates and nucleotide changes. I have spent way too much time trying to create a local mySQL instance of dbSNP from this site: https://cgsmd.isi.edu/dbsnpq/downloads.php#d ...
dbsnp coordinates genomic splice sites splice written 4.6 years ago by Parth Patel40

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