Hai,
I have a bam file and i need two fasta file, One is exactly mapped to reference and next one is not mapped to reference
How to do with samtools ?
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written
by
bioz •
The one with exact matches you already have, it's the reference fasta file you used for mapping. For the other fasta file, see the many questions like this and the links provided by Genomax: How to get the consensus sequence from a BAM alignment
I'm not provided with the used reference fasta file. Is there any way i could extract it from BAM file which was provided to me?
It should be apparent from the BAM header where the fasta file was from.
�BC]'�]M�6�Qv�Oa�l�?g�D@��P �Q�D )B�����m�U����w7���q���q\��ɏ��/����� }�w���/�������|��?��O���?����?�/�ǃ��K����Aj�b�ǃ�<�L�=h �R�����������Vz��$���| %����o�#�H��'��T�x���η�}�},@s�� ����R��� P ����/> ��K�|a��������&|�~�ŵV�����k��E~�)������ ��� �J������ ���K�O�J_��g���~�����>� 9�5W���� .�\U\��kv �;������WG I��j�ڒ�(a^�|�$5��74 H"��"v��?��s���5�����(��D� D�B����X����Q7*Q�5Ek<pa*5��d�,pq�#���\����� z�"�� �?��#���y�",�="" rl�{="" l`�?="" ����="" xb�nj�&�����.��}������?�Ǘ��i����ռ�cj�="" �uj���x r�nl<="" ��s$g�ޭ��a#r����="" <br=""/> \W 6��� ��� �Ш$'���[8��xa�s�a>�_��G�/��x�3S���y_3�9}>��.����<�y��Y�O��ϵ��}Q��1����Os��� ��A}��ϓp" �/� � F?$���� ��y��$ �m�c��jX this was the header when i tried to open the BAM file.
samtools view -H
@RG ID:SampleName_S1_L005_001_1 PL:ILLUMINA PU:SampleName_S1_L005_001_1 LB:SampleName_S1_L005_001 SM:SampleName_S1_L005_001
@PG ID:bwa CL:/usr/local/sentieon-genomics-201808/libexec/bwa mem -t 32 genome/hs38DH.fa /home/dnanexus/in/reads_fastqgzs/0/SampleName_S1_L005_R1_001.fastq.gz /home/dnanexus/in/reads2_fastqgzs/0/SampleName_S1_L005_R2_001.fastq.gz -K 100000000 -M -R @RG\tID:SampleName_S1_L005_001_1\tPL:ILLUMINA\tPU:SampleName_S1_L005_001_1\tLB:SampleName_S1_L005_001\tSM:SampleName_S1_L005_001 PN:bwa VN:0.7.15-r1140
@PG ID:sentieon-sort CL:/usr/local/sentieon-genomics-201808/libexec/util sort -o sorted_0.bam -t 32 --sam2bam --bam_compression 6 --block_size 2G -i - PN:sentieon-sort PP:bwa VN:sentieon-genomics-201808
@PG ID:sentieon-Dedup CL:/usr/local/sentieon-genomics-201808/libexec/driver --traverse_param 1000000/10000 -t 32 -i sorted_0.bam --algo Dedup --bam_compression 6 --score_info score.txt --metrics dedup_metrics.txt markdup.bam PN:sentieon-Dedup PP:sentieon-sort VN:sentieon-genomics-201808
Please help me find out!
That's hs38DH, which you can google for and probably comes from the 1000 genomes project.
Thank you so much.. I got it!
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