Missing SAM header when piping the samtools mpileup output to a VarScan call

Question

[melissachua90]

I want to run samtools and pipe the mpileup output into a VarScan call using the following conditions:

• 30 mapping score
• 30 phred quality score
• output-snp format
• min coverage = 50
• min tumor coverage = 3
• p-value = 0.01
• min variant frequency = 4%

Code:

samtools mpileup -B -q 30 -Q 30 -f hg19.fa normal_sort.bam tumor_sort.bam | java
-jar VarScan.v2.3.9.jar somatic /dev/stdin output --mpileup 1 --strand-filter 1 --output-snp --min-coverage 50 --min-coverage-tumor 3 --p-value 0.01 --min-var-freq 0.04

Traceback:

[E::sam_parse1] missing SAM header
[W::sam_read1] Parse error at line 1
Input file was not ready after 100 5-second cycles!

[Pierre Lindenbaum]

it's a problem with samtools mpileup -B -q 30 -Q 30 -f hg19.fa normal_sort.bam tumor_sort.bam not varscan.

check both commands output a header

samtools view -H normal_sort.bam 
samtools view -H tumor_sort.bam 

[melissachua90]

Seems like the normal_sort.bam is missing the header. What should I do about it?

samtools view -H normal_sort.bam
samtools view -H tumor_sort.bam
@SQ     SN:chr22        LN:51304566

[Pierre Lindenbaum]

check your upstream workflow, re-run.

[Ram]

Why did you delete the post, melissachua90?