Dear All,
I have a BAM file with reads from full genome sequencing
and I wanted to extract only reads that match exome sequencing reads
stored in my bed file.
1) here is the command that I used:
samtools view -b -L CTR9_FEB2015.merged.realigned.bed V54120.bam -o
exom.V54120.bam
So I got bam file that has only header lines
when checked using: samtools view -H exom.V54120.bam
but no reads! when trying : samtools view exom.V54120.bam
and indeed it is very small in size (5.4 Kb)
I am new to samtools and below is my short investigation which,
however, did not help ;(
I wonder whether I am missing something in my commands? Could anyone
help me with this?
Thank you!
First I tried to check whether anything can be retrieved from the bam file:
samtools view V54120.bam chr1:1000-2000
and got the following error message:
[main_samview] region "chr1:1000-2000" specifies an unknown reference
name. Continue anyway.
Then I checked chromosome names:
samtools view -H /gpfs/rocket/gv/V54120.bam | awk '/@SQ/'
@SQ SN:1 LN:249250621
UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta
AS:GRCh37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo
Sapiens
@SQ SN:2 LN:243199373
UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta
AS:GRCh37 M5:a0d9851da00400dec1098a9255ac712e SP:Homo
Sapiens
Then assuming that 'chr1' should be '1',I tried:
samtools view V54120.bam 3:1000-2000
this produced nothing ;(
no errors and no output to standard output
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