Finding number of reads and base calls at ~10,000 non-SNPs using BAM file?
I am working on paleogenomic data. I have BAM files from two different datasets that were processed/sequenced different. I am trying to look into some relationships between post-mortem damage and batch effects.
I have BAM files for each individual. I have ~10,000 sites where are monomorphic to reference in 1000G + SGDP (so I would think all non-reference calls are error).
I was wondering if anyone could recommend a way where I could probe BAM files to figure out number of total reads at each site as well number of alt reads. Thanks!
(It is also important to me to know where in the read that the base is, but I think that might overcomplicate things for now)
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
MD5 not the same between contig and reference; both Unified Genotyper and Haplotype Caller
written by j.lunger18 •
-
Analysing BAM files
written by User000
-
Comparison of transcripts of different parasite stages - graphic output
written by Heinrich_M •
-
Clipping reads within BAM files?
written by devenvyas
-
Finding # of UMIs with and without specific SNP
written by aalith •
-
Making BAM or SAM files equivalent
written by keturner123 •
-
why JGIL no output
written by wang.yiguan •
-
How to do genome guided denovo assembly? If not, how to align the denovo assembled bam to a particu…
written by kirannbishwa01
-
Missing reads in BAM to Fastq conversion
written by sergiogalvezrojas •
-
Extracting Genomic Coverage Information Across Different Samples
written by empyrean999
