Dear all,
I use cn.mops to call CNV in tumor-only samples, My data is Targeted DNA sequencing data.
Preparations:
I have prepared sorted bam file, bam index file and target region bed file. My bed file contains four columns(chromosome,start,end and name).
Command lines are as follows:
>library(cn.mops)
>BAMFiles <- list.files(pattern=".bam$")
>segments <- read.table("targetRegions.bed",sep="\t",as.is=TRUE)
>gr <- GRanges(segments[,1],IRanges(segments[,2],segments[,3]))
> X <- getSegmentReadCountsFromBAM(BAMFiles,GR=gr,mode="unpaired",)
and ran into this error infomation:
Processing S10_align_sorted.bam
Error in value[[3L]](cond) : 'countBam' failed:
record: 0
error: 0
file: S10_align_sorted.bam
index: S10_align_sorted.bam
In addition: Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
space 'chr21' not in BAM header
what is the reason, is it because I don't have a chromosome ref seq alignment information or something else?
Thank you for your time.
Hi, Gunter,
Thank you for your reply. I use samtools to check the header of my bam files. It's like this.
@HD VN:1.0 SO:coordinate
@SQ SN:chr21_16510183_16510354_25 LN:172
@SQ SN:chr19_42788849_42788989_CIC LN:141
@SQ SN:chr19_42790834_42790976_CIC LN:143
@SQ SN:chr19_42790921_42791078_CIC LN:158
@SQ SN:chr19_42791055_42791192_CIC LN:138
@SQ SN:chr19_42791130_42791304_CIC LN:175
@SQ SN:chr19_42791236_42791393_CIC LN:158
@SQ SN:chr19_42791375_42791514_CIC LN:140
@SQ SN:chr19_42791469_42791618_CIC LN:150
@SQ SN:chr19_42791548_42791705_CIC LN:158
@SQ SN:chr19_42791647_42791794_CIC LN:148
@SQ SN:chr19_42791726_42791896_CIC LN:171
@SQ SN:chr19_42791865_42792021_CIC LN:157
and my bed file is like this:
chr21 16510183 16510354 25
chr19 42788849 42788989 CIC
chr19 42790834 42790976 CIC
chr19 42790921 42791078 CIC
chr19 42791055 42791192 CIC
chr19 42791130 42791304 CIC
chr19 42791236 42791393 CIC
chr19 42791375 42791514 CIC
chr19 42791469 42791618 CIC
chr19 42791548 42791705 CIC
chr19 42791647 42791794 CIC
chr19 42791726 42791896 CIC
chr19 42791865 42792021 CIC
chr19 42792991 42793143 CIC
chr19 42793078 42793251 CIC
chr19 42793206 42793330 CIC
chr19 42793338 42793511 CIC
chr19 42793381 42793541 CIC
I have arranged the sam file and bed file in the same order. If this is what you want to check.
Best.
Seems like the sequence names are "chr19_42791865_42792021_CIC" rather than "chr19", that's why the function does not find any reads. Please check why this happens in your BAM file.
Thank you. Gunter. Problem has been solved. I generated a new reference with banner only have chrXXX.
Best regards,
Great, thanks for the heads-up!!