Samtools pileup problem.

Question

[salvatore.digiorgio]

Hi all,

I have problems with samtools command line:

for i in /Users/ECA/*.bam; do echo $i; samtools mpileup -t ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -Q 13 --max-idepth 8000 -l /Users/ECA_pos.bed -vuf /Users/Desktop/GRCh38/GRCh38.d1.vd1.fasta $i > $i_DE_TP.vcf; done

I generated a file.bed with my positions and it looks like follow, where the columns are tab separated.

chr7 117067403 117067666

chr6 117512942 117513865

chr2 131280907 131281440

chr5 131346892 131347779

I don't obtain any output file and I don't understand where is the problems.

Tanks SD

Answer 1

[Pierre Lindenbaum]

I bet your chromosomes in the BAM are named "1", "2", "3" and not "chr1", "chr2", "chr3". OR there is not read in those regions.

[salvatore.digiorgio]

I see reads with igv, and chromosome in BAM file are named "chr", I used same command line but with file.txt and single position and all was ok. It's very strange.

[Pierre Lindenbaum]

what are the chromosomes in the the output of

samtools view -H your.bam

?

[salvatore.digiorgio]

@SQ SN:chr1 LN:248956422 @SQ SN:chr2 LN:242193529