User: pfs

gravatar for pfs
pfs90
Reputation:
90
Status:
Trusted
Location:
USA/Boston
Last seen:
2 days, 11 hours ago
Joined:
2 months ago
Email:
f***************@gmail.com

Posts by pfs

<prev • 21 results • page 1 of 3 • next >
0
votes
3
answers
158
views
3
answers
Answer: A: How to make variant calling run faster?
... If speed is your main concern and tool development is not an option I would change my pipeline to use Samtools for variant calling. I have benchmark variant calling tools in the past and Samtools is a lot faster than GATK haplotypecaller v3.5. I can not speak for newer versions of GATK. ...
written 3 days ago by pfs90
0
votes
4
answers
167
views
4
answers
Answer: A: Compare between two columns of two different files and print common
... Untested but something like this should work: cut -f3 file1 > positions.txt; grep -wF position.txt file2 > File3 ...
written 5 days ago by pfs90
0
votes
4
answers
167
views
4
answers
Answer: A: Compare between two columns of two different files and print common
... What have you tried so far? ...
written 5 days ago by pfs90
2
votes
2
answers
135
views
2
answers
Answer: A: difference between 2 snp's data annotations
... Trust your data annotation. When you look up one SNP in dnSNP you will see that your annotation matches GRCh37 while the Scan annotation does not match GRCh38. https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=987435 Judging by data sources of information documented in the about SCAN link ...
written 10 days ago by pfs90
3
votes
2
answers
121
views
2
answers
Answer: A: How to find the unique list of mismatches of reads with the reference genome
... It looks like you need to implement a variant calling step and then do some data parsing to get your desired out put format. See http://www.htslib.org/workflow/ ...
written 11 days ago by pfs90
1
vote
3
answers
147
views
3
answers
Answer: A: Reference and mutant allele of a SNP rsID
... You could download the entire data set locally and either query it using a script or load it into a database and query it using a SQL statement. ftp://ftp.ncbi.nih.gov/snp/ ...
written 19 days ago by pfs90
0
votes
2
answers
161
views
2
answers
Comment: C: Indentical proteins but different Blast results
... Is the protein in question SCO2792? And what genome are you using? ...
written 26 days ago by pfs90
0
votes
2
answers
161
views
2
answers
Answer: A: Indentical proteins but different Blast results
... Any chance you are observing gene duplication? What is the % identity between different alignments? ...
written 26 days ago by pfs90
0
votes
1
answer
102
views
1
answers
Answer: A: Subsetting individuals in PLINK when IDs contain underscores "_"
... Plink documentation recommends converting underscores in an ID to a different character. Why not just use sed to change the underscores to another character? Below if from PLINK. https://www.cog-genomics.org/plink2/input The family and within-family IDs default to 'FAM001' and 'ID001' respectivel ...
written 26 days ago by pfs90
0
votes
3
answers
181
views
3
answers
Comment: C: Using Plink, get allele frequencies for a subset of individuals
... Can you double check the path to the --keep file and make sure this file has the expected number of lines (wc -l keep_file). What version of Plink are you running? ...
written 27 days ago by pfs90

Latest awards to pfs

Scholar 9 days ago, created an answer that has been accepted. For A: How to find the unique list of mismatches of reads with the reference genome
Scholar 9 days ago, created an answer that has been accepted. For A: How to find the unique list of mismatches of reads with the reference genome
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: How to find the unique list of mismatches of reads with the reference genome

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 955 users visited in the last hour