User: Bioscientist

gravatar for Bioscientist
Bioscientist1.6k
Reputation:
1,650
Status:
Trusted
Location:
Last seen:
6 years, 8 months ago
Joined:
7 years, 6 months ago
Email:
u2078

Posts by Bioscientist

<prev • 132 results • page 1 of 14 • next >
0
votes
1
answer
9.5k
views
1
answers
Comment: C: Gatk Multi-Sample Calling
... thanks! that makes sense! ...
written 6.7 years ago by Bioscientist1.6k
1
vote
1
answer
3.6k
views
1
answer
Calling Of Mutil-Allelic Snp Using Gatk
... I have four samples in a trio (and actually they are all patients) I tried using GATK-UnifiedGenotyper to call SNP/indel independently for each of them; as well as put them together and call SNP simultaneously. When I check how the program deal with multi-allelic SNP, I found sth. interesting: sam ...
gatk snp written 6.7 years ago by Bioscientist1.6k • updated 6.7 years ago by Jorge Amigo11k
0
votes
1
answer
9.5k
views
1
answers
Comment: C: Gatk Multi-Sample Calling
... thx, Alex; but plz see my edit. If I run bam files in trio independently, will results be different? ...
written 6.7 years ago by Bioscientist1.6k
6
votes
1
answer
9.5k
views
1
answer
Gatk Multi-Sample Calling
... I just want to know if my understanding is correct or not. So for multi-sample,to use GATK for SNP/indel calling, what I should do is: 1.Independently run BWA for alignment and mark duplicates; 2.Independently realign bam file, and do the recalibration. Then I got, say, A.recal.bam, B.recal.bam, C ...
gatk written 6.7 years ago by Bioscientist1.6k • updated 6.7 years ago by Alex Paciorkowski3.3k
0
votes
2
answers
6.8k
views
2
answers
Comment: C: How To Filter Against Common Snp Database To Look For Rare Variants?
... Also, the dbSNP, you mean all SNP, common SNP? There are two different database on UCSC, one "all SNP", one "common SNP" ...
written 6.7 years ago by Bioscientist1.6k
0
votes
2
answers
4.1k
views
2
answers
Comment: C: Snp Filtering After Being Called.
... THX....But just wanna say, GATK is sooooooooo complicated! It takes me > 10 steps to do realignment, fix mate pair, recalibrate, and calling SNP. And still tons of trick to filter them! ...
written 6.7 years ago by Bioscientist1.6k
8
votes
2
answers
4.1k
views
2
answers
Snp Filtering After Being Called.
... I'm now calling SNP using both samtools and GATK. To achieve a better specificity, I would guess: 1.Find the overlap between the two approach. (So will the # of callings of both be similar, or dramatically different?) 2.There's some other tools for filtering of SNP? btw, I think GATK is way much mu ...
filter samtools snp gatk written 6.7 years ago by Bioscientist1.6k • updated 5.3 years ago by Jorge Amigo11k
1
vote
1
answer
3.4k
views
1
answer
Dbsnp In Bed Format
... I've seen there are many format of dbSNP (XML or ASN1); I'm wondering if there's available bed format of dbSNP? Or from which format can I create the bed? Also, I can easily download bed format of SNP from UCSC genome. So any difference between the two? Should I merge them into a larger database? ...
dbsnp snp written 6.7 years ago by Bioscientist1.6k • updated 6.7 years ago by Vikas Bansal2.3k
0
votes
2
answers
6.8k
views
2
answers
Comment: C: How To Filter Against Common Snp Database To Look For Rare Variants?
... so basically you mean we should consider the change of base, rather than simply the position, right? thx ...
written 6.7 years ago by Bioscientist1.6k
3
votes
2
answers
6.8k
views
2
answers
How To Filter Against Common Snp Database To Look For Rare Variants?
... I've been using samtools/GATK to call for SNP/indels these days, and would like to filter my data against known common variants, to achieve rare events. Some of the samtools results can be: #CHROM POS ID REF ALT 1 10177 . ACCT ACCCT There could be several alternatives ...
samtools snp written 6.7 years ago by Bioscientist1.6k • updated 5 months ago by Biostar ♦♦ 20

Latest awards to Bioscientist

Voter 6.7 years ago, voted more than 100 times.
Centurion 6.7 years ago, created 100 posts.
Supporter 6.7 years ago, voted at least 25 times.
Guru 6.7 years ago, received more than 100 upvotes.
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Gatk Multi-Sample Calling
Popular Question 6.7 years ago, created a question with more than 1,000 views. For How To Filter Against Common Snp Database To Look For Rare Variants?
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Bwa Sampe Very Large Insert Size
Good Question 6.7 years ago, asked a question that was upvoted at least 5 times. For Is Dindel Still Preferred Over Gatk For Indel Calling?
Appreciated 6.7 years ago, created a post with more than 5 votes. For Is Dindel Still Preferred Over Gatk For Indel Calling?
Student 6.7 years ago, asked a question with at least 3 up-votes. For Is Dindel Still Preferred Over Gatk For Indel Calling?
Student 6.7 years ago, asked a question with at least 3 up-votes. For Softwares For Simple Statistics Of Bed Files
Appreciated 6.7 years ago, created a post with more than 5 votes. For Softwares For Simple Statistics Of Bed Files
Student 6.8 years ago, asked a question with at least 3 up-votes. For Connect Eqtl And Gwas Study
Student 6.9 years ago, asked a question with at least 3 up-votes. For Find Gene Symbol/Gene Name According To Orf Accession
Student 6.9 years ago, asked a question with at least 3 up-votes. For Softwares For Calculation Of Genome-Wide Alignments Coverage
Popular Question 6.9 years ago, created a question with more than 1,000 views. For Softwares For Calculation Of Genome-Wide Alignments Coverage
Popular Question 7.0 years ago, created a question with more than 1,000 views. For What Is Pcr Duplicates Of Ngs?
Student 7.0 years ago, asked a question with at least 3 up-votes. For Memory Usage Of Abyss Assembler
Popular Question 7.0 years ago, created a question with more than 1,000 views. For How Mapq In Bwa Is Calculated?
Student 7.0 years ago, asked a question with at least 3 up-votes. For How Mapq In Bwa Is Calculated?
Student 7.1 years ago, asked a question with at least 3 up-votes. For Bwa Seed Length
Popular Question 7.1 years ago, created a question with more than 1,000 views. For Fastq Format Problem When Using Bwa Aln -Q Option (Read Trim)
Student 7.1 years ago, asked a question with at least 3 up-votes. For Trim The Low-Quality End Of 100Bp Read

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 839 users visited in the last hour