User: Bioscientist
Bioscientist • 1.7k
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Posts by Bioscientist
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C: Gatk Multi-Sample Calling
... thanks! that makes sense! ...
written 8.5 years ago by
Bioscientist • 1.7k
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... 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 ...
written 8.5 years ago by
Bioscientist • 1.7k
• updated
8.5 years ago by
Jorge Amigo ♦ 12k
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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 8.5 years ago by
Bioscientist • 1.7k
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... 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 ...
written 8.5 years ago by
Bioscientist • 1.7k
• updated
8.5 years ago by
Alex Paciorkowski ♦ 3.4k
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... Also, the dbSNP, you mean all SNP, common SNP? There are two different database on UCSC, one "all SNP", one "common SNP" ...
written 8.5 years ago by
Bioscientist • 1.7k
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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 8.5 years ago by
Bioscientist • 1.7k
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... 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 ...
written 8.5 years ago by
Bioscientist • 1.7k
• updated
7.2 years ago by
Jorge Amigo ♦ 12k
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... 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?
...
written 8.5 years ago by
Bioscientist • 1.7k
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8.5 years ago by
Vikas Bansal • 2.4k
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... so basically you mean we should consider the change of base, rather than simply the position, right? thx ...
written 8.5 years ago by
Bioscientist • 1.7k
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... 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 ...
written 8.5 years ago by
Bioscientist • 1.7k
• updated
2.3 years ago by
Biostar ♦♦ 20
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For Gatk Multi-Sample Calling
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For How To Filter Against Common Snp Database To Look For Rare Variants?
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For Softwares For Simple Statistics Of Bed Files
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