Error encountered querying alignments: htsjdk.samtools.SAMFormatException: Invalid GZIP header

[Sakura Nussbaum]

Hello igv-help people,

I am not very familiar with IGV yet, but I have some trouble opening bam files.

1. I am using IVG 2.3.68 (and Java 8 Update 73)
   
2. I try to open bam files and to zoom (as I am asked to do).
   
3. I expect IVG to display my data, as it is on my colleague's laptop 
4. I got the following error message:  Error encountered querying alignments: htsjdk.samtools.SAMFormatException: Invalid GZIP header

Does someone know what could be the problem?

Cheers

[Sakura Nussbaum]

I also get this error message sometimes:  Error encountered querying alignments: java.lang.NullPointerException

[Sakura Nussbaum]

I tried to uninstall and install IGV again, but it is the same problem. I attached my igv.log file

Le lundi 7 mars 2016 11:25:45 UTC+9, Sakura Nussbaum a écrit :

[Jim Robinson]

The most likely cause is an invalid index for the BAM file.   It could also be a corrupt file.   Are you able to use this file with other tools,  for example "samtools view",  in the same genomic region as you encountered the error?

Jim

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[Sakura Nussbaum]

It was indeed an index problem! I used the samtools index command and it worked. I don't understand how it really works yet, but I guess I will learn little by little.

Thank you very much Jim!

[majidm...@gmail.com]

Dear james

I have same problem!

I can use my bam file with samtools view

also I can use my bam file in other samtools command for variant calling

can u help me?

در دوشنبه 7 مارس 2016، ساعت 7:59:21 (UTC+3:30)، James Robinson نوشته:

[James Robinson]

If it really is the same problem you can fix it by recomputing the index with samtools.     Sorry I can't really answer questions about variant calling,  perhaps ask on biostars or seqanswers.

[majid mojarrad]

Dear James

i recompute it with samtools but problem is still repeat.

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[majid mojarrad]

i use several bam file but all of them can not visualized by igv 

[majid mojarrad]

i use this commands

>samtools view -bS test.sam -o test.bam

>samtools sort test.bam test.sorted

>samtools index test.sorted.bam test.sorted.bam.bai

and use file (test.bam) in IGV

but it give error 

what can i do?

[James Robinson]

That is the correct procedure,  so I'm not really sure what the problem is.    If you can provide a test case I will look into it,  I will need the bam file and possibly the fasta file if its not one we host.

When making a bug report please include the IGV version number,  and your igv.log file.   

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[James Robinson]

Hi,

Sorry I missed this before.  But are you loading "test.bam"?   That is not going to work,  given your sequence of commands you should load  "test.sorted.bam".    I assume you just misstyped and meant to type "test.sorted.bam".

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[majid mojarrad]

hi 

i realy do this mistake😑

i load test.sorted.bam and this work

thank u very much indeed

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