Question: SAMTOOLS mpileup issues with TCGA data
1
gravatar for Vanish007
2.6 years ago by
Vanish00710
USA
Vanish00710 wrote:

Hi everyone,

Thanks for taking the time to read my question. Apologies in advance if I'm asking a basic question.

I'm currently trying to run Samtools mpileup and varscan on TCGA BAM files using the reference FASTA hg19.

samtools mpileup -f Homo_sapiens_assembly19.fasta Normal.rmdup.BAM Tumor.rmdup.BAM > Norm-Tum.mpileup

However I get a strange output after running the mpileup. Here is what the "head" command shows me for my .mpileup file:

1   10003   A   1   ^!. .   0   *   *
1   10004   C   1   .   <   0   *   *
1   10005   C   1   .   <   0       
1   10006   C   1   .   <   0       
1   10007   T   1   .   <   1   .   A
1   10008   A   2   ..  <3  1   .   =
1   10009   A   2   ..  <3  1   .   B
1   10010   C   2   ..  <3  3   .^/.^>. DAF
1   10011   C   2   ..  <3  3   ... EBE
1   10012   C   2   ..  <3  3   T.. CEF

Varscan2 completes almost as soon as I execute it and I'm left with only the headers with nothing in them: chrom chr_start chr_stop num_positions normal_depth tumor_depth log2_ratio gc_content

Any idea on what could be causing this? I'm currently using "Homo_sapiens_assembly19.fasta" as my reference. I also wanted to note that the BAM file doesn't seem to have the "chr" notation, instead only uses "SN:1, SN:2, etc". Would I have to change the chr notation in my BAM file for mpileup to work?

Apologies for the long post and thanks for reading.

ADD COMMENTlink modified 2.6 years ago by geek_y9.3k • written 2.6 years ago by Vanish00710
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