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ANGSD / angsd

Program for analysing NGS data.
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Error: No header information could be found for BAM/CRAM file #324

Closed mgb1985 closed 2 years ago

mgb1985 commented 4 years ago

Hi!

I want to generate SFS for plenty of samples listed in bam.list.

I use this script:

ref2019='/home/myref.fa'
mapq='30'    # min MapQ
minq='20'    # min Q
while read indv; do
angsd -i $indv -anc $ref2019 -dosaf 1 -GL 2 -fold 1 -minMapQ $mapq -minQ $minq -out $indv
#realSFS $indv\.saf.idx > $indv|.sfs
done < bam.list

I get the error: No header information could be found for BAM/CRAM file

I don't understand what is the issue? Strangely, when I use the list to generate a population SFS (using -bam option instead of -i), it is working.

What can I do?

Thanks,

Mgb

ANGSD commented 4 years ago

So -i is for multiple samples -b is for a file list. -b is short for -bam.

But the sfs code has been updated quite alot recently so either pull the latest version of angsd or wait a few days til im finished updating it.

On 9 Jun 2020, at 13.45, mgb1985 notifications@github.com wrote:

Hi!

I want to generate SFS for plenty of samples listed in bam.list.

I use this script:

ref2019='/home/myref.fa' mapq='30' # min MapQ minq='20' # min Q while read indv; do angsd -i $indv -anc $ref2019 -dosaf 1 -GL 2 -fold 1 -minMapQ $mapq -minQ $minq -out $indv

realSFS $indv.saf.idx > $indv|.sfs

done < bam.list I get the error: No header information could be found for BAM/CRAM file

I don't understand what is the issue? Strangely, when I use the list to generate a population SFS (using -bam option instead of -i), it is working.

What can I do?

Thanks,

Mgb

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mgb1985 commented 4 years ago

So -i is for multiple samples -b is for a file list. -b is short for -bam. But the sfs code has been updated quite alot recently so either pull the latest version of angsd or wait a few days til im finished updating it. …

Thanks for your reply. I think I misunderstood -i. How can I do to generate a SFS on each bam listed in my bam.list?

The script I provided above is not OK?

Thanks,

ANGSD commented 2 years ago

You can find documentation here: http://www.popgen.dk/angsd/index.php/SFS_Estimation

I am closing this issue, feel free to reopen if needed.