This looks great! I will try that. Thank you very much!
• 0 views
•
link
written
by
katrina.eaton •
Filter reads by SNP by genotype
I am trying to filter files by the specific genotype at a specific SNP. Example: I want all the reads with a "T" in position chr1:181188090. Everything I've seen so far is looking at the quality of the reads, but that's already been addressed.
This can't be that difficult, clearly I'm missing something, but I don't know what. Any help would be greatly appreciated.
• 1,580 views
•
link
updated
by
GenoMax
•
written
by
katrina.eaton •
•
written
by
katrina.eaton •
1 answer
How about @Pierre's solution here: How to extract reads with a known variant form a bam file
Log in to answer this question.
More posts like this
-
Missing ATP Synthase Genes in TCGA Dataset
written by bucksotj •
-
I need to extract the FASTA reads from a specific region from a chromosome in a BAM file format.
written by screadore •
-
Need help figuring out all the possible combinations of genotypes for SNPs in ancient DNA sample
written by amandaskinner94 •
-
How to do SNP selection in large VCF/BCF/GenotypeTables in R like you can using BCFTools,CYVCF2 or …
written by William
-
Filtering multisample vcf file by
written by devin.porter92 •
-
HTSJDK help, how to randomaccess a position and count read counts in a bam file?
written by ylaguka •
-
Filter VCF on Number of genotyped individuals
written by mek362 •
-
How to handle missing values when combining multiple VCF files?
written by Ruyang •
-
Need Help Interpreting The Genotype Fields In A Vcf Formatted Data
written by CrazyB
-
Snp Genotype Data
written by Haluk
Assuming you have the BAM file you could extract all reads that overlap an interval that contains that SNP and then filter for the specific position. e.g. Extract Reads From A Bam File That Fall Within A Given Region and extract reads from BAM whose fragments overlap a specified region
I have a bam file that has all the reads that overlap the interval in question, the part I can't figure out is how to filter for only the reads that have a T at that position.
To elaborate: I'm looking at a maternal plasma sample, and am trying to isolate the fetal fraction. I have SNPs where I know what the genotype is, and the fetus has one allele different from the mother. I'm trying to isolate the fetal reads, to then determine the read length.
The filtration examples I've seen have been for quality or some other metric, I'm struggling to find a way to get a stream of nucleotides from that one position to filter.