Chromosomal notation and Segmentation fault

meher · 04-17-2013, 02:36 AM

Hi all,

I have a bam file with chromosomal notation 1,2.... and i need it to be as chr1,chr2.....

For this i have tried, samtools view -H sample.bam > header.sam

Then edited the header.sam file with required chromosomal notation and tried samtools reheader header.sam sample.bam > out.bam

when in tried to view out.bam using samtools it says "Segemntation fault".

I also tried with PICARD, java -Xmx4g -jar ReplaceSamHeader.jar INPUT=sample.bam HEADER=header.sam OUTPUT=out.bam CREATE_INDEX=TRUE

It reports the same error with samtools i.e. segmenation fault.

Could anyone help me to fix this?

wangwl · 07-29-2013, 07:19 PM

I got the same problem...

Finally i gave up the reheader option. and use " cat header.sam sample.sam | samools view -S -b - >sample.bam" instead.

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04-17-2013, 02:36 AM	#1
meher Member Location: helsinki Join Date: Jun 2011 Posts: 54	Chromosomal notation and Segmentation fault Hi all, I have a bam file with chromosomal notation 1,2.... and i need it to be as chr1,chr2..... For this i have tried, samtools view -H sample.bam > header.sam Then edited the header.sam file with required chromosomal notation and tried samtools reheader header.sam sample.bam > out.bam when in tried to view out.bam using samtools it says "Segemntation fault". I also tried with PICARD, java -Xmx4g -jar ReplaceSamHeader.jar INPUT=sample.bam HEADER=header.sam OUTPUT=out.bam CREATE_INDEX=TRUE It reports the same error with samtools i.e. segmenation fault. Could anyone help me to fix this?

07-29-2013, 07:19 PM	#2
wangwl Junior Member Location: China Join Date: Aug 2012 Posts: 1	I got the same problem... Finally i gave up the reheader option. and use " cat header.sam sample.sam \| samools view -S -b - >sample.bam" instead. Last edited by wangwl; 07-29-2013 at 07:32 PM.