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.
