Question: Problem in generating hc.readcount files using bam-readcount
0
gravatar for Rahil
23 months ago by
Rahil170
Rahil170 wrote:

Hi, I want to run fpfilter (VarScan false-positive filter) to remove false positives from the vcf files; however I stuck in the step of generating readcount from my vcf file. This is my command:

bam-readcount  -f hg38.fa  -q 1  -b 20  -l all.Somatic.hc.var  tumor.sorted.bam > all.Somatic.hc.readcount

I get this error:

Minimum mapping quality is set to 1
[bam_index_load] fail to load BAM index.
BAM indexing file is not available.

Can anyone help me out? Thanks!

ADD COMMENTlink modified 23 months ago by ATpoint40k • written 23 months ago by Rahil170
0
gravatar for ATpoint
23 months ago by
ATpoint40k
Germany
ATpoint40k wrote:

Index the Bam file as clearly stated in the error message. samtools index in.bam

ADD COMMENTlink written 23 months ago by ATpoint40k

Thank you ATpoint, I did your suggestion but still I get error. I indexed the sorted.bam file samtools index tumor.sorted.bam and put the output tumor.sorted.bam.bai in the command

bam-readcount  -f hg38.fa  -q 1  -b 20  -l all.Somatic.hc.var  tumor.sorted.bam.bai > all.Somatic.hc.readcount

I got this error:

[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Segmentation fault (core dumped)

Any help?

ADD REPLYlink written 23 months ago by Rahil170

No, you supply the Bam file in the command. The index file only needs to be present in the same directory. Please spend some time on searching around for the basics of NGS file formats and its usage.

ADD REPLYlink written 23 months ago by ATpoint40k
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