Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
The tools you're using just report the SNPs found in your data. You'll have to assign the SNPs the dbSNP data with another tool, e.g. GATK VariantAnnotator, to which you provide the dbSNP entries as a file.
Leave a comment:
-
samtools mpileup and bcftools not reporting dbSNP ids
The vcf output after running mpileup and bcftools seems to fail to report dbSNP ids. Here are the commands I used against my BAM file...pretty much identical to the example code provided with the mpileup documentation.
samtools mpileup -ugf /data/genomes/hg19/hg19.fa aln.bam > aln_varRaw.bcf
bcftools view -cvg aln_varRaw.bcf | vcfutils.pl varFilter -D100 > aln.vcf
And here are the first 10 lines of the output vcf file.
chr1 16571 . G A 3.02 . AF1=1.000;AFE=0.375;DP4=0,0,0,1;MQ=30 PL:GT:GQ 30,3,0:1/1:41
chr1 74817 . G A 3.02 . AF1=1.000;AFE=0.375;DP4=0,0,0,1;MQ=30 PL:GT:GQ 30,3,0:1/1:41
chr1 118617 . T C 3.02 . AF1=1.000;AFE=0.375;DP4=0,0,1,0;MQ=30 PL:GT:GQ 30,3,0:1/1:41
chr1 231504 . G A 23.8 . AF1=1.000;AFE=0.829;DP4=0,0,2,0;MQ=30 PL:GT:GQ 55,6,0:1/1:49
chr1 232960 . C A 11.1 . AF1=1.000;AFE=0.768;DP4=0,0,0,2;MQ=30 PL:GT:GQ 42,6,0:1/1:49
chr1 233473 . C G 4.13 . AF1=0.500;AFE=0.307;DP4=1,1,2,0;MQ=30;PV4=1,0.0048,1,0.23 PL:GT:GQ 32,0,48:0/1:35
chr1 235976 . C A 52 . AF1=1.000;AFE=0.899;DP4=0,0,2,1;MQ=30 PL:GT:GQ 84,9,0:1/1:63
chr1 726481 . T G 13.9 . AF1=1.000;AFE=0.799;DP4=0,0,2,0;MQ=30 PL:GT:GQ 45,6,0:1/1:49
chr1 726939 . G C 14.9 . AF1=1.000;AFE=0.806;DP4=0,0,1,1;MQ=30 PL:GT:GQ 46,6,0:1/1:49
chr1 726944 . C G 21.8 . AF1=1.000;AFE=0.827;DP4=0,0,1,1;MQ=30 PL:GT:GQ 53,6,0:1/1:49
I realize that these 10 calls may not have a match in dbSNP but NONE of my calls have an associated rsID. rsID should be listed in the 3rd column.
I looked for specific parameters for setting up a connection to dbSNP but I cannot seem to find that information. Seems like I'm missing something.
Thanks.
Dan
Latest Articles
Collapse
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:37 PM
|
0 responses
11 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
10 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
51 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
67 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Leave a comment: