Entering edit mode
2.5 years ago
melissachua90
▴
70
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!
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
Seems like the
normal_sort.bam
is missing the header. What should I do about it?check your upstream workflow, re-run.
Why did you delete the post, melissachua90?